diff --git a/README.md b/README.md index 880106c..6bce6c9 100644 --- a/README.md +++ b/README.md @@ -85,3 +85,25 @@ Output: - Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong, C. H., Khor, C. C., Petric, R., Hibberd, M. L., & Nagarajan, N. (2012). LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Research, 40(22), 11189–11201. https://doi.org/10.1093/nar/gks918 - Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., Gurfield, N., Van Rompay, K. K. A., Isern, S., Michael, S. F., Coffey, L. L., Loman, N. J., & Andersen, K. G. (2019). An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology, 20(1), 8. https://doi.org/10.1186/s13059-018-1618-7 - Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560 + + +## Known issues + +The variant normalization workflow may appear as corrupt when calling to it concurrently. +A workaround to this situation is to clone the tronflow dependencies and let covigator pipeline know of the location of the `main.nf` files. + +For instance: +``` +cd /covigator/dependencies +git clone --branch v1.4.0 https://github.com/TRON-Bioinformatics/tronflow-bwa.git +git clone --branch v1.5.0 https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing.git +git clone --branch v1.1.0 https://github.com/TRON-Bioinformatics/tronflow-variant-normalization.git +``` + +And then use the following parameters: +``` +nextflow run tron-bioinformatics/covigator-ngs-pipeline -profile conda \ +--tronflow_bwa /covigator/dependencies/tronflow-bwa/main.nf \ +--tronflow_bam_preprocessing /covigator/dependencies/tronflow-bam-preprocessing/main.nf \ +--tronflow_variant_normalization /covigator/dependencies/tronflow-variant-normalization/main.nf ... +``` \ No newline at end of file diff --git a/benchmark/ERR5229917/ERR5229917.annotated.vcf b/benchmark/ERR5229917/ERR5229917.annotated.vcf deleted file mode 100644 index 4db464f..0000000 --- a/benchmark/ERR5229917/ERR5229917.annotated.vcf +++ /dev/null @@ -1,72 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5229917.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5229917.vcf; Date=Mon Jun 7 15:46:05 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:46:17 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5229917.normalized.vcf -; Date=Mon Jun 7 15:46:17 2021 -##bcftools/csqVersion=1.12+htslib-1.12 -##bcftools/csqCommand=csq --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --gff-annot /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.101.gff3 -o ERR5229917.annotated.vcf /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5229917.normalized.vcf; Date=Mon Jun 7 15:46:19 2021 -##INFO= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=131;VDB=1.4224e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,78,48;MQ=60 GT:PL:AD 1:255,0:0,126 -MN908947.3 913 . C T 225.417 . DP=129;VDB=6.20234e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,52;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|216S|913C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|216S|913C>T GT:PL:AD:BCSQ 1:255,0:0,127:5 -MN908947.3 3037 . C T 225.417 . DP=111;VDB=4.91991e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,53;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|924F|3037C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|924F|3037C>T GT:PL:AD:BCSQ 1:255,0:0,108:5 -MN908947.3 3177 . C T 228.395 . DP=72;VDB=1;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,41,28;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|971P>971L|3177C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|971P>971L|3177C>T GT:PL:AD:BCSQ 1:255,0:1,69:5 -MN908947.3 3267 . C T 225.417 . DP=113;VDB=0.000108359;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,70,38;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1001T>1001I|3267C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1001T>1001I|3267C>T GT:PL:AD:BCSQ 1:255,0:0,108:5 -MN908947.3 5388 . C A 225.417 . DP=109;VDB=0.000332757;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,41;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1708A>1708D|5388C>A,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1708A>1708D|5388C>A GT:PL:AD:BCSQ 1:255,0:0,107:5 -MN908947.3 5986 . C T 225.417 . DP=77;VDB=1.57378e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,45,28;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1907F|5986C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1907F|5986C>T GT:PL:AD:BCSQ 1:255,0:0,73:5 -MN908947.3 6954 . T C 225.417 . DP=111;VDB=1.06073e-08;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,53;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2230I>2230T|6954T>C,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2230I>2230T|6954T>C GT:PL:AD:BCSQ 1:255,0:0,109:5 -MN908947.3 11287 . GTCTGGTTTT G 228.393 . INDEL;IDV=132;IMF=0.94964;DP=139;VDB=1.88453e-08;SGB=-0.693147;MQSB=0.979246;MQ0F=0;AC=1;AN=1;DP4=5,2,87,45;MQ=59;BCSQ=inframe_deletion|ORF1ab|ENSSAST00005000003|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G,inframe_deletion|ORF1ab|ENSSAST00005000002|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G GT:PL:AD:BCSQ 1:255,0:7,132:5 -MN908947.3 11296 . T G 14.5687 . DP=3;VDB=0.14;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,2,0;MQ=60 GT:PL:AD 1:44,0:0,2 -MN908947.3 14408 . C T 225.417 . DP=125;VDB=1.43995e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,46;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4715L|14408C>T GT:PL:AD:BCSQ 1:255,0:0,119:1 -MN908947.3 14676 . C T 228.409 . DP=121;VDB=1.56534e-06;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,83,34;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|4804P>4801L|14676C>T GT:PL:AD:BCSQ 1:255,0:1,117:1 -MN908947.3 15279 . C T 225.417 . DP=98;VDB=0.00245807;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,69,27;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5005T>5002I|15279C>T GT:PL:AD:BCSQ 1:255,0:0,96:1 -MN908947.3 16176 . T C 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,21;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5304L>5301P|16176T>C GT:PL:AD:BCSQ 1:255,0:0,80:1 -MN908947.3 21764 . ATACATG A 225.421 . INDEL;IDV=60;IMF=1;DP=60;VDB=1.55058e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,22;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGTCT|ATCT;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|68IHV>68I|21764ATACATG>A GT:PL:AD:BCSQ 1:255,0:0,59:1 -MN908947.3 21990 . TTTA T 178.235 . INDEL;IDV=43;IMF=0.843137;DP=51;VDB=0.999998;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=6,3,27,15;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|143VY>141V|21990TTTA>T GT:PL:AD:BCSQ 1:255,50:9,42:1 -MN908947.3 23063 . A T 225.417 . DP=90;VDB=0.111568;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,28;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|501N>498Y|23063A>T GT:PL:AD:BCSQ 1:255,0:0,79:1 -MN908947.3 23271 . C A 228.41 . DP=126;VDB=0.000148154;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,81,39;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|570A>567D|23271C>A GT:PL:AD:BCSQ 1:255,0:1,120:1 -MN908947.3 23403 . A G 225.417 . DP=142;VDB=8.79877e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,91,47;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|614D>611G|23403A>G GT:PL:AD:BCSQ 1:255,0:0,138:1 -MN908947.3 23604 . C A 225.417 . DP=109;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,44;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|681P>678H|23604C>A GT:PL:AD:BCSQ 1:255,0:0,104:1 -MN908947.3 23709 . C T 225.417 . DP=79;VDB=8.52388e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,30,48;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|716T>713I|23709C>T GT:PL:AD:BCSQ 1:255,0:0,78:1 -MN908947.3 24506 . T G 225.417 . DP=103;VDB=0.0210185;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,33;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|982S>979A|24506T>G GT:PL:AD:BCSQ 1:255,0:0,97:1 -MN908947.3 24914 . G C 225.417 . DP=141;VDB=0.00368073;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,48;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|1118D>1115H|24914G>C GT:PL:AD:BCSQ 1:255,0:0,134:1 -MN908947.3 27972 . C T 225.417 . DP=95;VDB=0.00177412;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,40;MQ=60;BCSQ=stop_gained|ORF8|ENSSAST00005000008|protein_coding|+|27Q>27*|27972C>T GT:PL:AD:BCSQ 1:255,0:0,91:1 -MN908947.3 28048 . G T 225.417 . DP=94;VDB=0.00104892;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,46;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|52R>52I|28048G>T GT:PL:AD:BCSQ 1:255,0:0,92:1 -MN908947.3 28111 . A G 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,32;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|73Y>73C|28111A>G GT:PL:AD:BCSQ 1:255,0:0,79:1 -MN908947.3 28270 . TA T 59.0943 . INDEL;IDV=121;IMF=0.937984;DP=129;VDB=0.000210326;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=9,8,73,39;MQ=60;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:86,0:17,112 -MN908947.3 28274 . A T 9.88514 . DP=122;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60;BCSQ=start_lost|N|ENSSAST00005000005|protein_coding|+ GT:PL:AD:BCSQ 1:39,0:0,1:1 -MN908947.3 28280 . G C 225.417 . DP=120;VDB=8.64822e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|3D>3L|28280G>C+28281A>T+28282T>A GT:PL:AD:BCSQ 1:255,0:0,119:1 -MN908947.3 28281 . A T 225.417 . DP=120;VDB=8.10825e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,119:1 -MN908947.3 28282 . T A 225.417 . DP=120;VDB=6.34296e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,119:1 -MN908947.3 28881 . G A 225.417 . DP=108;VDB=3.77072e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,46;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|203R>203K|28881G>A+28882G>A GT:PL:AD:BCSQ 1:255,0:0,105:1 -MN908947.3 28882 . G A 225.417 . DP=107;VDB=1.39355e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60;BCSQ=@28881 GT:PL:AD:BCSQ 1:255,0:0,105:1 -MN908947.3 28883 . G C 225.417 . DP=108;VDB=1.29056e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|204G>204R|28883G>C GT:PL:AD:BCSQ 1:255,0:0,105:1 -MN908947.3 28977 . C T 225.417 . DP=69;VDB=0.305786;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,14,55;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|235S>235F|28977C>T GT:PL:AD:BCSQ 1:255,0:0,69:1 diff --git a/benchmark/ERR5229917/ERR5229917.normalized.vcf b/benchmark/ERR5229917/ERR5229917.normalized.vcf deleted file mode 100644 index a5945b5..0000000 --- a/benchmark/ERR5229917/ERR5229917.normalized.vcf +++ /dev/null @@ -1,68 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5229917.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5229917.vcf; Date=Mon Jun 7 15:46:05 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:46:17 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5229917.normalized.vcf -; Date=Mon Jun 7 15:46:17 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=131;VDB=1.4224e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,78,48;MQ=60 GT:PL:AD 1:255,0:0,126 -MN908947.3 913 . C T 225.417 . DP=129;VDB=6.20234e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,52;MQ=60 GT:PL:AD 1:255,0:0,127 -MN908947.3 3037 . C T 225.417 . DP=111;VDB=4.91991e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,53;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 3177 . C T 228.395 . DP=72;VDB=1;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,41,28;MQ=60 GT:PL:AD 1:255,0:1,69 -MN908947.3 3267 . C T 225.417 . DP=113;VDB=0.000108359;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,70,38;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 5388 . C A 225.417 . DP=109;VDB=0.000332757;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,41;MQ=60 GT:PL:AD 1:255,0:0,107 -MN908947.3 5986 . C T 225.417 . DP=77;VDB=1.57378e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,45,28;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 6954 . T C 225.417 . DP=111;VDB=1.06073e-08;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,53;MQ=60 GT:PL:AD 1:255,0:0,109 -MN908947.3 11287 . GTCTGGTTTT G 228.393 . INDEL;IDV=132;IMF=0.94964;DP=139;VDB=1.88453e-08;SGB=-0.693147;MQSB=0.979246;MQ0F=0;AC=1;AN=1;DP4=5,2,87,45;MQ=59 GT:PL:AD 1:255,0:7,132 -MN908947.3 11296 . T G 14.5687 . DP=3;VDB=0.14;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,2,0;MQ=60 GT:PL:AD 1:44,0:0,2 -MN908947.3 14408 . C T 225.417 . DP=125;VDB=1.43995e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,46;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 14676 . C T 228.409 . DP=121;VDB=1.56534e-06;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,83,34;MQ=60 GT:PL:AD 1:255,0:1,117 -MN908947.3 15279 . C T 225.417 . DP=98;VDB=0.00245807;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,69,27;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 16176 . T C 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,21;MQ=60 GT:PL:AD 1:255,0:0,80 -MN908947.3 21764 . ATACATG A 225.421 . INDEL;IDV=60;IMF=1;DP=60;VDB=1.55058e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,22;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGTCT|ATCT GT:PL:AD 1:255,0:0,59 -MN908947.3 21990 . TTTA T 178.235 . INDEL;IDV=43;IMF=0.843137;DP=51;VDB=0.999998;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=6,3,27,15;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA GT:PL:AD 1:255,50:9,42 -MN908947.3 23063 . A T 225.417 . DP=90;VDB=0.111568;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,28;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 23271 . C A 228.41 . DP=126;VDB=0.000148154;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,81,39;MQ=60 GT:PL:AD 1:255,0:1,120 -MN908947.3 23403 . A G 225.417 . DP=142;VDB=8.79877e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,91,47;MQ=60 GT:PL:AD 1:255,0:0,138 -MN908947.3 23604 . C A 225.417 . DP=109;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,44;MQ=60 GT:PL:AD 1:255,0:0,104 -MN908947.3 23709 . C T 225.417 . DP=79;VDB=8.52388e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,30,48;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 24506 . T G 225.417 . DP=103;VDB=0.0210185;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,33;MQ=60 GT:PL:AD 1:255,0:0,97 -MN908947.3 24914 . G C 225.417 . DP=141;VDB=0.00368073;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,48;MQ=60 GT:PL:AD 1:255,0:0,134 -MN908947.3 27972 . C T 225.417 . DP=95;VDB=0.00177412;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,40;MQ=60 GT:PL:AD 1:255,0:0,91 -MN908947.3 28048 . G T 225.417 . DP=94;VDB=0.00104892;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,46;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 28111 . A G 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,32;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 28270 . TA T 59.0943 . INDEL;IDV=121;IMF=0.937984;DP=129;VDB=0.000210326;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=9,8,73,39;MQ=60;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:86,0:17,112 -MN908947.3 28274 . A T 9.88514 . DP=122;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:39,0:0,1 -MN908947.3 28280 . G C 225.417 . DP=120;VDB=8.64822e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28281 . A T 225.417 . DP=120;VDB=8.10825e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28282 . T A 225.417 . DP=120;VDB=6.34296e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28881 . G A 225.417 . DP=108;VDB=3.77072e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,46;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28882 . G A 225.417 . DP=107;VDB=1.39355e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28883 . G C 225.417 . DP=108;VDB=1.29056e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28977 . C T 225.417 . DP=69;VDB=0.305786;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,14,55;MQ=60 GT:PL:AD 1:255,0:0,69 diff --git a/benchmark/ERR5229917/ERR5229917.preprocessed.gatk.vcf b/benchmark/ERR5229917/ERR5229917.preprocessed.gatk.vcf deleted file mode 100644 index 6d03f93..0000000 --- a/benchmark/ERR5229917/ERR5229917.preprocessed.gatk.vcf +++ /dev/null @@ -1,59 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 20615.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.412;DP=792;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.33;ReadPosRankSum=-1.516;SOR=0.768 GT:AD:DP:GQ:PL 1:2,781:783:99:20625,0 -MN908947.3 913 . C T 26006.04 . AC=1;AF=1.00;AN=1;DP=943;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.36;SOR=0.960 GT:AD:DP:GQ:PL 1:0,917:917:99:26016,0 -MN908947.3 3037 . C T 22783.04 . AC=1;AF=1.00;AN=1;DP=802;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.59;SOR=0.954 GT:AD:DP:GQ:PL 1:0,797:797:99:22793,0 -MN908947.3 3177 . C T 16932.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.220;DP=546;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.69;ReadPosRankSum=2.370;SOR=0.934 GT:AD:DP:GQ:PL 1:2,516:518:99:16942,0 -MN908947.3 3267 . C T 30517.04 . AC=1;AF=1.00;AN=1;DP=1140;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.05;SOR=0.726 GT:AD:DP:GQ:PL 1:0,1128:1128:99:30527,0 -MN908947.3 5388 . C A 28935.04 . AC=1;AF=1.00;AN=1;DP=1090;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.72;SOR=0.702 GT:AD:DP:GQ:PL 1:0,1083:1083:99:28945,0 -MN908947.3 5986 . C T 16464.04 . AC=1;AF=1.00;AN=1;DP=583;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.29;SOR=0.971 GT:AD:DP:GQ:PL 1:0,582:582:99:16474,0 -MN908947.3 6954 . T C 19560.04 . AC=1;AF=1.00;AN=1;DP=727;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.94;SOR=0.815 GT:AD:DP:GQ:PL 1:0,726:726:99:19570,0 -MN908947.3 11287 . GTCTGGTTTT G 61583.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.756;DP=1439;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;MQRankSum=-0.019;QD=36.91;ReadPosRankSum=-0.650;SOR=1.169 GT:AD:DP:GQ:PL 1:2,1372:1374:99:61593,0 -MN908947.3 14408 . C T 28437.04 . AC=1;AF=1.00;AN=1;DP=1075;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.75;SOR=0.737 GT:AD:DP:GQ:PL 1:0,1063:1063:99:28447,0 -MN908947.3 14676 . C T 35524.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.682;DP=1352;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.49;ReadPosRankSum=-1.547;SOR=0.716 GT:AD:DP:GQ:PL 1:6,1335:1341:99:35534,0 -MN908947.3 15279 . C T 30572.04 . AC=1;AF=1.00;AN=1;DP=1069;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.68;SOR=0.898 GT:AD:DP:GQ:PL 1:0,1066:1066:99:30582,0 -MN908947.3 16176 . T C 28502.04 . AC=1;AF=1.00;AN=1;DP=930;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.76;SOR=0.707 GT:AD:DP:GQ:PL 1:0,870:870:99:28512,0 -MN908947.3 21764 . ATACATG A 11934.04 . AC=1;AF=1.00;AN=1;DP=481;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.70;SOR=0.907 GT:AD:DP:GQ:PL 1:0,447:447:99:19914,0 -MN908947.3 21990 . TTTA T 11149.01 . AC=1;AF=1.00;AN=1;DP=270;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.92;SOR=0.701 GT:AD:DP:GQ:PL 1:0,249:249:99:11159,0 -MN908947.3 23063 . A T 7247.04 . AC=1;AF=1.00;AN=1;DP=266;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.45;SOR=0.693 GT:AD:DP:GQ:PL 1:0,264:264:99:7257,0 -MN908947.3 23271 . C A 30270.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.462;DP=1141;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.95;ReadPosRankSum=1.909;SOR=0.728 GT:AD:DP:GQ:PL 1:4,1119:1123:99:30280,0 -MN908947.3 23403 . A G 32369.04 . AC=1;AF=1.00;AN=1;DP=1154;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.65;SOR=0.979 GT:AD:DP:GQ:PL 1:0,1130:1130:99:32379,0 -MN908947.3 23604 . C A 25556.04 . AC=1;AF=1.00;AN=1;DP=958;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.73;SOR=0.745 GT:AD:DP:GQ:PL 1:0,956:956:99:25566,0 -MN908947.3 23709 . C T 20648.04 . AC=1;AF=1.00;AN=1;DP=556;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.16;SOR=3.144 GT:AD:DP:GQ:PL 1:0,552:552:99:20658,0 -MN908947.3 24506 . T G 22899.04 . AC=1;AF=1.00;AN=1;DP=803;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.55;SOR=0.889 GT:AD:DP:GQ:PL 1:0,802:802:99:22909,0 -MN908947.3 24914 . G C 32418.04 . AC=1;AF=1.00;AN=1;DP=1233;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.62;SOR=0.726 GT:AD:DP:GQ:PL 1:0,1218:1218:99:32428,0 -MN908947.3 27972 . C T 12886.04 . AC=1;AF=1.00;AN=1;DP=498;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.73;SOR=0.735 GT:AD:DP:GQ:PL 1:0,482:482:99:12896,0 -MN908947.3 28048 . G T 11014.04 . AC=1;AF=1.00;AN=1;DP=403;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.33;SOR=0.749 GT:AD:DP:GQ:PL 1:0,403:403:99:11024,0 -MN908947.3 28111 . A G 16509.04 . AC=1;AF=1.00;AN=1;DP=516;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.35;SOR=1.247 GT:AD:DP:GQ:PL 1:0,495:495:99:16519,0 -MN908947.3 28270 . TA T 46893.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.429;DP=1068;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.36;ReadPosRankSum=1.760;SOR=0.707 GT:AD:DP:GQ:PL 1:2,1049:1051:99:46903,0 -MN908947.3 28280 . G C 27666.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.445;DP=1043;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.53;ReadPosRankSum=1.497;SOR=0.697 GT:AD:DP:GQ:PL 1:2,1041:1043:99:46493,0 -MN908947.3 28281 . A T 46277.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.445;DP=1050;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.13;ReadPosRankSum=1.482;SOR=0.697 GT:AD:DP:GQ:PL 1:2,1035:1037:99:46287,0 -MN908947.3 28282 . T A 27520.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.445;DP=1050;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.54;ReadPosRankSum=1.435;SOR=0.697 GT:AD:DP:GQ:PL 1:2,1035:1037:99:46287,0 -MN908947.3 28881 . G A 14684.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.482;DP=575;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.81;ReadPosRankSum=2.321;SOR=0.771 GT:AD:DP:GQ:PL 1:2,567:569:99:25218,0 -MN908947.3 28882 . G A 14709.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.456;DP=576;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.85;ReadPosRankSum=2.331;SOR=0.771 GT:AD:DP:GQ:PL 1:2,567:569:99:25218,0 -MN908947.3 28883 . G C 14732.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.474;DP=571;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.89;ReadPosRankSum=2.371;SOR=0.771 GT:AD:DP:GQ:PL 1:2,567:569:99:25216,0 -MN908947.3 28977 . C T 10330.04 . AC=1;AF=1.00;AN=1;DP=259;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=35.27;SOR=4.255 GT:AD:DP:GQ:PL 1:0,250:250:99:10340,0 diff --git a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated.vcf b/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated.vcf deleted file mode 100644 index a39048c..0000000 --- a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated.vcf +++ /dev/null @@ -1,278 +0,0 @@ -##fileformat=VCFv4.0 -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5229917/ERR5229917.preprocessed.lofreq.vcf ERR5229917/ERR5229917.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" -##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-intergenic -no-intron SARS-COV2 ERR5229917/ERR5229917.preprocessed.lofreq.vcf " -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 173 . CG C 72.0 PASS DP=760;AF=0.005263;SB=0;DP4=406,352,2,2;INDEL;HRUN=1 -MN908947.3 241 . C T 29888.0 PASS DP=800;AF=0.995000;SB=0;DP4=1,1,390,406 -MN908947.3 283 . TG T 74.0 PASS DP=726;AF=0.005510;SB=0;DP4=337,385,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20delG|p.Gly7fs|20/21290|20/21290|7/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 336 . G A 136.0 PASS DP=610;AF=0.018033;SB=1;DP4=251,345,4,7;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.71G>A|p.Arg24His|71/21290|71/21290|24/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 370 . G C 63.0 PASS DP=662;AF=0.007553;SB=6;DP4=314,341,4,1;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.105G>C|p.Val35Val|105/21290|105/21290|35/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 376 . G T 61.0 PASS DP=671;AF=0.007452;SB=0;DP4=347,317,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.111G>T|p.Glu37Asp|111/21290|111/21290|37/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 377 . G GC 52.0 PASS DP=659;AF=0.004552;SB=0;DP4=346,322,2,1;INDEL;HRUN=1;ANN=GC|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.112_113insC|p.Val38fs|113/21290|113/21290|38/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 419 . G T 72.0 PASS DP=634;AF=0.007886;SB=0;DP4=379,250,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.154G>T|p.Gly52Cys|154/21290|154/21290|52/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 509 . GGTCATGTTATGGTT G 70.0 PASS DP=914;AF=0.004376;SB=0;DP4=458,452,2,2;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/21290|246/21290|82/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 534 . CAG C 71.0 PASS DP=902;AF=0.004435;SB=0;DP4=447,457,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.271_272delGA|p.Glu91fs|271/21290|271/21290|91/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 536 . G T 83.0 PASS DP=901;AF=0.006659;SB=0;DP4=439,450,3,3;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.271G>T|p.Glu91*|271/21290|271/21290|91/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 738 . AAG A 97.0 PASS DP=712;AF=0.007022;SB=3;DP4=404,303,4,1;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.475_476delGA|p.Glu159fs|475/21290|475/21290|159/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 794 . CT C 110.0 PASS DP=1051;AF=0.005709;SB=0;DP4=534,513,3,3;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.531delT|p.Asn178fs|531/21290|531/21290|177/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 884 . CG C 68.0 PASS DP=1049;AF=0.003813;SB=0;DP4=515,536,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.620delG|p.Arg207fs|620/21290|620/21290|207/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 899 . T A 136.0 PASS DP=1023;AF=0.009775;SB=1;DP4=487,526,4,6;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.634T>A|p.Ser212Thr|634/21290|634/21290|212/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 900 . C A 134.0 PASS DP=1018;AF=0.009823;SB=1;DP4=480,528,4,6;ANN=A|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.635C>A|p.Ser212*|635/21290|635/21290|212/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 913 . C T 35817.0 PASS DP=931;AF=1.000000;SB=0;DP4=0,0,417,514;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.648C>T|p.Ser216Ser|648/21290|648/21290|216/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 931 . TG T 156.0 PASS DP=844;AF=0.009479;SB=0;DP4=354,492,3,5;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.667delG|p.Asp223fs|667/21290|667/21290|223/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1027 . T C 81.0 PASS DP=544;AF=0.011029;SB=1;DP4=320,218,3,3;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.762T>C|p.Pro254Pro|762/21290|762/21290|254/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1104 . T C 127.0 PASS DP=708;AF=0.011299;SB=0;DP4=346,354,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.839T>C|p.Ile280Thr|839/21290|839/21290|280/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1216 . T G 305.0 PASS DP=537;AF=0.029795;SB=3;DP4=222,299,5,11;ANN=G|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.951T>G|p.Leu317Leu|951/21290|951/21290|317/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1302 . C T 62.0 PASS DP=350;AF=0.011429;SB=0;DP4=155,191,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1037C>T|p.Thr346Ile|1037/21290|1037/21290|346/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1406 . G T 61.0 PASS DP=445;AF=0.008989;SB=0;DP4=222,216,2,2;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1141G>T|p.Glu381*|1141/21290|1141/21290|381/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1720 . TG T 54.0 PASS DP=596;AF=0.005034;SB=0;DP4=302,289,2,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1456delG|p.Ala486fs|1456/21290|1456/21290|486/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 1813 . T TA 112.0 PASS DP=593;AF=0.013491;SB=0;DP4=290,295,4,4;INDEL;HRUN=6;ANN=TA|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1554dupA|p.Gly519fs|1555/21290|1555/21290|519/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2157 . T C 61.0 PASS DP=341;AF=0.011730;SB=0;DP4=141,196,2,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1892T>C|p.Leu631Pro|1892/21290|1892/21290|631/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2229 . G T 63.0 PASS DP=287;AF=0.013937;SB=0;DP4=155,128,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1964G>T|p.Cys655Phe|1964/21290|1964/21290|655/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2365 . TA T 55.0 PASS DP=609;AF=0.004926;SB=2;DP4=313,295,1,2;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2103delA|p.Ala702fs|2103/21290|2103/21290|701/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2403 . CA C 82.0 PASS DP=672;AF=0.008929;SB=0;DP4=337,329,3,3;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2141delA|p.Lys714fs|2141/21290|2141/21290|714/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2557 . AC A 80.0 PASS DP=511;AF=0.007828;SB=0;DP4=265,242,2,2;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2294delC|p.Pro765fs|2294/21290|2294/21290|765/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2644 . C T 100.0 PASS DP=855;AF=0.008187;SB=0;DP4=446,402,4,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2379C>T|p.Ile793Ile|2379/21290|2379/21290|793/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2714 . G T 77.0 PASS DP=981;AF=0.006116;SB=0;DP4=488,487,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2449G>T|p.Gly817Cys|2449/21290|2449/21290|817/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2777 . AGT A 74.0 PASS DP=754;AF=0.005305;SB=0;DP4=327,427,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2516_2517delTG|p.Val839fs|2516/21290|2516/21290|839/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2889 . TG T 86.0 PASS DP=704;AF=0.008523;SB=10;DP4=394,304,1,5;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2626delG|p.Ala876fs|2626/21290|2626/21290|876/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 3037 . C T 31757.0 PASS DP=825;AF=1.000000;SB=0;DP4=0,0,371,454;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2772C>T|p.Phe924Phe|2772/21290|2772/21290|924/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3177 . C T 19987.0 PASS DP=545;AF=0.990826;SB=0;DP4=1,1,304,239;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2912C>T|p.Pro971Leu|2912/21290|2912/21290|971/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3239 . G T 63.0 PASS DP=872;AF=0.005734;SB=1;DP4=509,358,4,1;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2974G>T|p.Asp992Tyr|2974/21290|2974/21290|992/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3250 . G C 79.0 PASS DP=967;AF=0.006205;SB=0;DP4=535,422,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2985G>C|p.Glu995Asp|2985/21290|2985/21290|995/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3267 . C T 43568.0 PASS DP=1150;AF=0.998261;SB=0;DP4=0,0,590,560;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3002C>T|p.Thr1001Ile|3002/21290|3002/21290|1001/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3549 . G C 63.0 PASS DP=334;AF=0.011976;SB=0;DP4=187,143,2,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3284G>C|p.Gly1095Ala|3284/21290|3284/21290|1095/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3557 . A G 64.0 PASS DP=363;AF=0.011019;SB=0;DP4=197,162,2,2;ANN=G|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3292A>G|p.Lys1098Glu|3292/21290|3292/21290|1098/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3768 . C T 68.0 PASS DP=221;AF=0.018100;SB=2;DP4=73,144,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3503C>T|p.Thr1168Ile|3503/21290|3503/21290|1168/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3802 . TA T 56.0 PASS DP=359;AF=0.008357;SB=0;DP4=238,127,2,1;INDEL;HRUN=5;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3542delA|p.Asn1181fs|3542/21290|3542/21290|1181/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 3837 . TG T 84.0 PASS DP=405;AF=0.009877;SB=2;DP4=270,131,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3574delG|p.Glu1192fs|3574/21290|3574/21290|1192/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4147 . TG T 73.0 PASS DP=762;AF=0.005249;SB=2;DP4=412,351,3,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3883delG|p.Val1295fs|3883/21290|3883/21290|1295/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4189 . CA C 70.0 PASS DP=907;AF=0.004410;SB=0;DP4=469,435,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3925delA|p.Thr1309fs|3925/21290|3925/21290|1309/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4254 . CG C 69.0 PASS DP=969;AF=0.004128;SB=0;DP4=495,472,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3992delG|p.Gly1331fs|3992/21290|3992/21290|1331/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4290 . CA C 71.0 PASS DP=895;AF=0.004469;SB=0;DP4=443,448,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4028delA|p.Lys1343fs|4028/21290|4028/21290|1343/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4398 . TG T 70.0 PASS DP=942;AF=0.004246;SB=0;DP4=471,468,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4134delG|p.Met1378fs|4134/21290|4134/21290|1378/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5388 . C A 42501.0 PASS DP=1107;AF=1.000000;SB=0;DP4=0,0,559,548;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5123C>A|p.Ala1708Asp|5123/21290|5123/21290|1708/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 5530 . TG T 109.0 PASS DP=1099;AF=0.005460;SB=1;DP4=487,606,2,4;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5267delG|p.Gly1756fs|5267/21290|5267/21290|1756/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5706 . ATG A 61.0 PASS DP=1419;AF=0.002819;SB=4;DP4=716,700,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5442_5443delTG|p.Tyr1814fs|5442/21290|5442/21290|1814/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5744 . T C 66.0 PASS DP=1517;AF=0.003955;SB=0;DP4=764,745,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5479T>C|p.Tyr1827His|5479/21290|5479/21290|1827/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 5770 . CTA C 62.0 PASS DP=1503;AF=0.002661;SB=0;DP4=772,737,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5508_5509delTA|p.Tyr1836fs|5508/21290|5508/21290|1836/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5986 . C T 21855.0 PASS DP=582;AF=1.000000;SB=0;DP4=0,0,327,255;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5721C>T|p.Phe1907Phe|5721/21290|5721/21290|1907/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6180 . AT A 62.0 PASS DP=593;AF=0.006745;SB=0;DP4=271,319,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5916delT|p.Tyr1972fs|5916/21290|5916/21290|1972/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6241 . G C 82.0 PASS DP=1297;AF=0.005397;SB=0;DP4=758,532,4,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5976G>C|p.Trp1992Cys|5976/21290|5976/21290|1992/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6330 . C CA 58.0 PASS DP=1890;AF=0.002116;SB=0;DP4=957,929,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6068dupA|p.Asn2023fs|6069/21290|6069/21290|2023/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6388 . C T 64.0 PASS DP=1851;AF=0.003241;SB=0;DP4=922,923,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6123C>T|p.Cys2041Cys|6123/21290|6123/21290|2041/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6437 . CAG C 63.0 PASS DP=1422;AF=0.002813;SB=0;DP4=591,843,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6174_6175delGA|p.Lys2059fs|6174/21290|6174/21290|2058/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6445 . CG C 64.0 PASS DP=1323;AF=0.003023;SB=1;DP4=531,801,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6181delG|p.Val2061fs|6181/21290|6181/21290|2061/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6655 . TAATAGTGTCCCTTGGGATACTATAGCTA T 152.0 PASS DP=1155;AF=0.006926;SB=0;DP4=572,577,4,4;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6392_6419delATAGTGTCCCTTGGGATACTATAGCTAA|p.Asn2131fs|6392/21290|6392/21290|2131/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6696 . C CT 103.0 PASS DP=1114;AF=0.005386;SB=3;DP4=563,558,2,4;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6435dupT|p.Leu2146fs|6436/21290|6436/21290|2146/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6954 . T C 28841.0 PASS DP=750;AF=0.998667;SB=0;DP4=0,0,358,392;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6689T>C|p.Ile2230Thr|6689/21290|6689/21290|2230/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 7462 . TG T 108.0 PASS DP=986;AF=0.006085;SB=0;DP4=480,502,3,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7198delG|p.Val2400fs|7198/21290|7198/21290|2400/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 7640 . TG T 57.0 PASS DP=516;AF=0.005814;SB=0;DP4=216,297,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7376delG|p.Cys2459fs|7376/21290|7376/21290|2459/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 7948 . CAG C 77.0 PASS DP=571;AF=0.007005;SB=2;DP4=207,403,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7684_7685delAG|p.Gln2563fs|7684/21290|7684/21290|2562/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8128 . AAAG A 58.0 PASS DP=1839;AF=0.002175;SB=0;DP4=919,918,2,2;INDEL;HRUN=3;ANN=A|disruptive_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7866_7868delGAA|p.Lys2622del|7866/21290|7866/21290|2622/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 8133 . ATG A 58.0 PASS DP=1862;AF=0.002148;SB=0;DP4=932,930,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7872_7873delGT|p.Ser2625fs|7872/21290|7872/21290|2624/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8187 . T C 121.0 PASS DP=1758;AF=0.005688;SB=0;DP4=855,891,5,5;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7922T>C|p.Phe2641Ser|7922/21290|7922/21290|2641/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 8345 . TG T 55.0 PASS DP=484;AF=0.006198;SB=2;DP4=330,151,3,0;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8081delG|p.Cys2694fs|8081/21290|8081/21290|2694/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8430 . CTG C 73.0 PASS DP=799;AF=0.005006;SB=0;DP4=397,398,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8166_8167delTG|p.Glu2723fs|8166/21290|8166/21290|2722/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8945 . AAC A 57.0 PASS DP=530;AF=0.005660;SB=2;DP4=253,278,2,1;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8682_8683delCA|p.Ile2895fs|8682/21290|8682/21290|2894/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9250 . TG T 93.0 PASS DP=729;AF=0.008230;SB=0;DP4=424,301,4,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8986delG|p.Val2996fs|8986/21290|8986/21290|2996/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9314 . G T 75.0 PASS DP=1245;AF=0.005622;SB=0;DP4=667,568,4,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9049G>T|p.Val3017Phe|9049/21290|9049/21290|3017/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 9319 . CTG C 65.0 PASS DP=1275;AF=0.003137;SB=0;DP4=678,595,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9057_9058delTG|p.Cys3019fs|9057/21290|9057/21290|3019/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9331 . TG T 53.0 PASS DP=1434;AF=0.002789;SB=0;DP4=732,707,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9067delG|p.Ala3023fs|9067/21290|9067/21290|3023/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9583 . TG T 69.0 PASS DP=991;AF=0.004036;SB=0;DP4=569,418,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9319delG|p.Val3107fs|9319/21290|9319/21290|3107/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9790 . TG T 69.0 PASS DP=617;AF=0.006483;SB=2;DP4=219,396,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9526delG|p.Glu3176fs|9526/21290|9526/21290|3176/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9801 . CG C 127.0 PASS DP=663;AF=0.010558;SB=0;DP4=254,404,3,4;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9537delG|p.Leu3180fs|9537/21290|9537/21290|3179/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10426 . TG T 56.0 PASS DP=1096;AF=0.003650;SB=2;DP4=567,527,3,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10162delG|p.Val3388fs|10162/21290|10162/21290|3388/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10427 . G T 80.0 PASS DP=1116;AF=0.006272;SB=0;DP4=578,527,4,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10162G>T|p.Val3388Phe|10162/21290|10162/21290|3388/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 10527 . CT C 91.0 PASS DP=1435;AF=0.004181;SB=0;DP4=737,694,3,3;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10267delT|p.Cys3423fs|10267/21290|10267/21290|3423/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10625 . GCA G 64.0 PASS DP=1358;AF=0.002946;SB=0;DP4=658,711,2,2;INDEL;HRUN=1;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10363_10364delCA|p.Gln3455fs|10363/21290|10363/21290|3455/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10776 . C T 66.0 PASS DP=767;AF=0.006519;SB=3;DP4=442,320,4,1;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10511C>T|p.Pro3504Leu|10511/21290|10511/21290|3504/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 10880 . ATG A 69.0 PASS DP=995;AF=0.004020;SB=0;DP4=478,513,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10616_10617delTG|p.Met3539fs|10616/21290|10616/21290|3539/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11028 . T C 101.0 PASS DP=696;AF=0.010057;SB=3;DP4=366,322,5,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10763T>C|p.Leu3588Ser|10763/21290|10763/21290|3588/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11107 . TG T 82.0 PASS DP=1407;AF=0.003554;SB=0;DP4=790,612,3,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10843delG|p.Ala3615fs|10843/21290|10843/21290|3615/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11121 . T C 75.0 PASS DP=1745;AF=0.004011;SB=0;DP4=920,814,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10856T>C|p.Ile3619Thr|10856/21290|10856/21290|3619/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11138 . G T 68.0 PASS DP=1893;AF=0.004226;SB=0;DP4=945,936,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10873G>T|p.Ala3625Ser|10873/21290|10873/21290|3625/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11145 . TG T 58.0 PASS DP=1923;AF=0.002080;SB=0;DP4=962,957,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10881delG|p.Met3627fs|10881/21290|10881/21290|3627/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11175 . G GT 57.0 PASS DP=2019;AF=0.001981;SB=0;DP4=1002,1013,2,2;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10913dupT|p.Leu3638fs|10914/21290|10914/21290|3638/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11236 . TAG T 57.0 PASS DP=1972;AF=0.002028;SB=0;DP4=969,999,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10972_10973delAG|p.Ser3658fs|10972/21290|10972/21290|3658/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11287 . GTCTGGTTTT G 45483.0 PASS DP=1355;AF=0.996310;SB=71;DP4=69,33,541,809;INDEL;HRUN=1;ANN=G|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11023_11031delTCTGGTTTT|p.Ser3675_Phe3677del|11023/21290|11023/21290|3675/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11482 . TG T 67.0 PASS DP=1097;AF=0.003646;SB=0;DP4=572,521,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11218delG|p.Val3740fs|11218/21290|11218/21290|3740/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11615 . TG T 83.0 PASS DP=1330;AF=0.003759;SB=0;DP4=747,579,3,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11351delG|p.Cys3784fs|11351/21290|11351/21290|3784/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11693 . GT G 62.0 PASS DP=1515;AF=0.002640;SB=0;DP4=757,770,2,2;INDEL;HRUN=3;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11431delT|p.Tyr3811fs|11431/21290|11431/21290|3811/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11722 . G GT 80.0 PASS DP=1580;AF=0.003165;SB=1;DP4=775,805,3,2;INDEL;HRUN=3;ANN=GT|frameshift_variant&stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11460dupT|p.Arg3821fs|11461/21290|11461/21290|3821/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11741 . CAG C 61.0 PASS DP=1546;AF=0.002587;SB=0;DP4=756,791,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11477_11478delAG|p.Gln3826fs|11477/21290|11477/21290|3826/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11750 . C T 229.0 PASS DP=1577;AF=0.010146;SB=0;DP4=757,803,8,8;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11485C>T|p.Leu3829Phe|11485/21290|11485/21290|3829/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12233 . G A 71.0 PASS DP=1396;AF=0.004298;SB=0;DP4=672,718,3,3;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11968G>A|p.Glu3990Lys|11968/21290|11968/21290|3990/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12333 . CA C 60.0 PASS DP=1311;AF=0.003051;SB=0;DP4=640,669,2,2;INDEL;HRUN=4;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12072delA|p.Val4025fs|12072/21290|12072/21290|4024/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12396 . C T 248.0 PASS DP=971;AF=0.015448;SB=2;DP4=392,564,5,10;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12131C>T|p.Ala4044Val|12131/21290|12131/21290|4044/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12400 . C T 97.0 PASS DP=952;AF=0.007353;SB=0;DP4=384,561,3,4;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12135C>T|p.Leu4045Leu|12135/21290|12135/21290|4045/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12459 . C T 61.0 PASS DP=877;AF=0.005701;SB=4;DP4=524,346,2,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12194C>T|p.Thr4065Ile|12194/21290|12194/21290|4065/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12602 . G A 71.0 PASS DP=1484;AF=0.004043;SB=0;DP4=767,711,3,3;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12337G>A|p.Glu4113Lys|12337/21290|12337/21290|4113/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12646 . TG T 62.0 PASS DP=1468;AF=0.002725;SB=0;DP4=742,722,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12382delG|p.Val4128fs|12382/21290|12382/21290|4128/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12720 . TG T 69.0 PASS DP=968;AF=0.004132;SB=1;DP4=367,603,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12456delG|p.Met4152fs|12456/21290|12456/21290|4152/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12911 . G A 429.0 PASS DP=1478;AF=0.017591;SB=4;DP4=729,723,16,10;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12646G>A|p.Val4216Ile|12646/21290|12646/21290|4216/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13115 . C T 64.0 PASS DP=1874;AF=0.003202;SB=0;DP4=1080,788,4,2;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12850C>T|p.Leu4284Leu|12850/21290|12850/21290|4284/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13141 . TAA T 72.0 PASS DP=2254;AF=0.002218;SB=1;DP4=1155,1098,2,3;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12877_12878delAA|p.Asn4293fs|12877/21290|12877/21290|4293/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13182 . A AG 53.0 PASS DP=2541;AF=0.001574;SB=0;DP4=1303,1234,2,2;INDEL;HRUN=2;ANN=AG|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12919dupG|p.Ala4307fs|12920/21290|12920/21290|4307/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13345 . TG T 199.0 PASS DP=1348;AF=0.008160;SB=0;DP4=557,783,4,7;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13081delG|p.Val4361fs|13081/21290|13081/21290|4361/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13725 . TG T 50.0 PASS DP=802;AF=0.004988;SB=0;DP4=431,367,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13461delG|p.Leu4488fs|13461/21290|13461/21290|4487/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13812 . G T 131.0 PASS DP=1017;AF=0.008850;SB=1;DP4=533,475,4,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13547G>T|p.Trp4516Leu|13547/21290|13547/21290|4516/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13978 . G C 149.0 PASS DP=763;AF=0.013106;SB=2;DP4=417,330,7,3;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13713G>C|p.Val4571Val|13713/21290|13713/21290|4571/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13978 . G T 78.0 PASS DP=763;AF=0.007864;SB=0;DP4=417,330,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13713G>T|p.Val4571Val|13713/21290|13713/21290|4571/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13993 . G T 63.0 PASS DP=865;AF=0.005780;SB=1;DP4=470,388,2,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13728G>T|p.Lys4576Asn|13728/21290|13728/21290|4576/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14099 . G C 104.0 PASS DP=1246;AF=0.006421;SB=0;DP4=576,653,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13834G>C|p.Val4612Leu|13834/21290|13834/21290|4612/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14408 . C T 42523.0 PASS DP=1109;AF=0.996393;SB=0;DP4=0,0,553,553;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14143C>T|p.Leu4715Leu|14143/21290|14143/21290|4715/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14571 . C T 126.0 PASS DP=691;AF=0.013025;SB=1;DP4=363,319,4,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14306C>T|p.Thr4769Ile|14306/21290|14306/21290|4769/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14676 . C T 49314.0 PASS DP=1416;AF=0.995763;SB=0;DP4=3,3,718,692;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14411C>T|p.Pro4804Leu|14411/21290|14411/21290|4804/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14708 . CTG C 62.0 PASS DP=1464;AF=0.002732;SB=0;DP4=736,724,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14447_14448delGT|p.Cys4816fs|14447/21290|14447/21290|4816/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15202 . G T 82.0 PASS DP=711;AF=0.008439;SB=1;DP4=410,294,3,3;ANN=T|stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14937G>T|p.Ter4979Tyrext*?|14937/21290|14937/21290|4979/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15279 . C T 41710.0 PASS DP=1117;AF=0.998209;SB=0;DP4=0,0,615,502;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15014C>T|p.Thr5005Ile|15014/21290|15014/21290|5005/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15317 . T C 70.0 PASS DP=1380;AF=0.004348;SB=0;DP4=695,679,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15052T>C|p.Cys5018Arg|15052/21290|15052/21290|5018/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15441 . CATG C 88.0 PASS DP=1081;AF=0.004625;SB=0;DP4=470,607,2,3;INDEL;HRUN=1;ANN=C|disruptive_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15177_15179delATG|p.Cys5060del|15177/21290|15177/21290|5059/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15443 . TG T 88.0 PASS DP=1062;AF=0.004708;SB=0;DP4=463,601,2,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15179delG|p.Cys5060fs|15179/21290|15179/21290|5060/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15960 . CG C 61.0 PASS DP=1602;AF=0.002497;SB=0;DP4=809,791,2,2;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15697delG|p.Ala5233fs|15697/21290|15697/21290|5233/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15983 . TA T 53.0 PASS DP=1662;AF=0.002407;SB=0;DP4=824,834,2,2;INDEL;HRUN=5;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15723delA|p.Lys5241fs|15723/21290|15723/21290|5241/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16072 . G T 67.0 PASS DP=1609;AF=0.003729;SB=0;DP4=772,829,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15807G>T|p.Met5269Ile|15807/21290|15807/21290|5269/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16074 . TG T 140.0 PASS DP=1578;AF=0.005070;SB=0;DP4=758,814,4,4;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15810delG|p.Met5271fs|15810/21290|15810/21290|5270/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16111 . C T 69.0 PASS DP=1218;AF=0.004926;SB=1;DP4=478,734,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15846C>T|p.Ser5282Ser|15846/21290|15846/21290|5282/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16114 . CATG C 86.0 PASS DP=1195;AF=0.004184;SB=0;DP4=472,721,2,3;INDEL;HRUN=1;ANN=C|disruptive_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15854_15856delTGA|p.Met5285del|15854/21290|15854/21290|5285/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 16176 . T C 32264.0 PASS DP=875;AF=0.998857;SB=0;DP4=0,0,446,429;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15911T>C|p.Leu5304Pro|15911/21290|15911/21290|5304/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16191 . A T 82.0 PASS DP=676;AF=0.008876;SB=1;DP4=397,269,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15926A>T|p.Asn5309Ile|15926/21290|15926/21290|5309/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16324 . TG T 67.0 PASS DP=1124;AF=0.003559;SB=0;DP4=518,602,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16060delG|p.Val5354fs|16060/21290|16060/21290|5354/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16564 . G C 76.0 PASS DP=1179;AF=0.005089;SB=0;DP4=667,505,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16299G>C|p.Leu5433Phe|16299/21290|16299/21290|5433/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16647 . G C 68.0 PASS DP=1411;AF=0.004252;SB=0;DP4=709,696,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16382G>C|p.Arg5461Pro|16382/21290|16382/21290|5461/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16787 . G T 103.0 PASS DP=1082;AF=0.007394;SB=5;DP4=540,533,6,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16522G>T|p.Val5508Phe|16522/21290|16522/21290|5508/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16852 . G T 131.0 PASS DP=1422;AF=0.007032;SB=0;DP4=826,586,6,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16587G>T|p.Met5529Ile|16587/21290|16587/21290|5529/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17178 . TG T 56.0 PASS DP=1685;AF=0.002374;SB=0;DP4=973,711,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16914delG|p.Met5639fs|16914/21290|16914/21290|5638/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17193 . G T 88.0 PASS DP=2032;AF=0.003937;SB=0;DP4=1046,976,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16928G>T|p.Arg5643Ile|16928/21290|16928/21290|5643/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17201 . TA T 53.0 PASS DP=2074;AF=0.001929;SB=0;DP4=1057,1015,2,2;INDEL;HRUN=4;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16940delA|p.Asn5647fs|16940/21290|16940/21290|5647/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17247 . TG T 55.0 PASS DP=2191;AF=0.001826;SB=0;DP4=1102,1085,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16983delG|p.Leu5662fs|16983/21290|16983/21290|5661/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17274 . CA C 67.0 PASS DP=2190;AF=0.002740;SB=0;DP4=1089,1098,3,3;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17012delA|p.Lys5671fs|17012/21290|17012/21290|5671/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17320 . G T 88.0 PASS DP=2074;AF=0.003857;SB=0;DP4=1027,1039,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17055G>T|p.Met5685Ile|17055/21290|17055/21290|5685/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17329 . G T 63.0 PASS DP=1902;AF=0.003155;SB=0;DP4=902,994,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17064G>T|p.Leu5688Leu|17064/21290|17064/21290|5688/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17338 . G T 61.0 PASS DP=1753;AF=0.003423;SB=0;DP4=789,957,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17073G>T|p.Gln5691His|17073/21290|17073/21290|5691/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17339 . CAG C 58.0 PASS DP=1715;AF=0.002332;SB=4;DP4=786,962,3,1;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17076_17077delGA|p.Gln5692fs|17076/21290|17076/21290|5692/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17359 . G T 70.0 PASS DP=1510;AF=0.003974;SB=0;DP4=645,859,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17094G>T|p.Met5698Ile|17094/21290|17094/21290|5698/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17569 . CCTG C 105.0 PASS DP=1273;AF=0.004713;SB=0;DP4=625,642,3,3;INDEL;HRUN=2;ANN=C|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17308_17310delCTG|p.Leu5770del|17308/21290|17308/21290|5770/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 17704 . AG A 53.0 PASS DP=735;AF=0.004082;SB=5;DP4=284,450,0,3;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17441delG|p.Gly5814fs|17441/21290|17441/21290|5814/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17727 . AG A 74.0 PASS DP=726;AF=0.005510;SB=1;DP4=312,411,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17463delG|p.Asn5822fs|17463/21290|17463/21290|5821/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17749 . G T 84.0 PASS DP=622;AF=0.009646;SB=0;DP4=340,276,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17484G>T|p.Leu5828Leu|17484/21290|17484/21290|5828/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18290 . G T 260.0 PASS DP=1061;AF=0.016023;SB=6;DP4=569,475,12,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18025G>T|p.Val6009Leu|18025/21290|18025/21290|6009/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18395 . CTG C 62.0 PASS DP=1423;AF=0.002811;SB=1;DP4=845,578,3,1;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18132_18133delGT|p.Tyr6045fs|18132/21290|18132/21290|6044/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 18443 . G T 95.0 PASS DP=1810;AF=0.004420;SB=0;DP4=927,873,4,4;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18178G>T|p.Glu6060*|18178/21290|18178/21290|6060/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18530 . TA T 61.0 PASS DP=1589;AF=0.002517;SB=0;DP4=737,861,2,2;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18268delA|p.Arg6090fs|18268/21290|18268/21290|6090/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 18668 . G T 66.0 PASS DP=776;AF=0.006443;SB=0;DP4=468,302,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18403G>T|p.Val6135Leu|18403/21290|18403/21290|6135/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18858 . TG T 68.0 PASS DP=1044;AF=0.003831;SB=0;DP4=494,551,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18594delG|p.Met6198fs|18594/21290|18594/21290|6198/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 19177 . G C 81.0 PASS DP=935;AF=0.006417;SB=0;DP4=376,552,2,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18912G>C|p.Met6304Ile|18912/21290|18912/21290|6304/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19794 . G T 81.0 PASS DP=928;AF=0.006466;SB=0;DP4=459,463,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19529G>T|p.Gly6510Val|19529/21290|19529/21290|6510/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19860 . TG T 75.0 PASS DP=676;AF=0.005917;SB=1;DP4=277,395,1,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19596delG|p.Leu6533fs|19596/21290|19596/21290|6532/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 19937 . A G 142.0 PASS DP=414;AF=0.019324;SB=3;DP4=275,130,5,4;ANN=G|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19672A>G|p.Thr6558Ala|19672/21290|19672/21290|6558/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19983 . C CT 82.0 PASS DP=517;AF=0.011605;SB=0;DP4=318,195,4,2;INDEL;HRUN=6;ANN=CT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19724dupT|p.Leu6575fs|19725/21290|19725/21290|6575/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20029 . GC G 79.0 PASS DP=548;AF=0.007299;SB=0;DP4=320,225,2,2;INDEL;HRUN=3;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19767delC|p.Val6590fs|19767/21290|19767/21290|6589/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20133 . CG C 60.0 PASS DP=416;AF=0.007212;SB=0;DP4=159,254,1,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19869delG|p.Ter6624fs|19869/21290|19869/21290|6623/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20680 . G A 83.0 PASS DP=645;AF=0.009302;SB=0;DP4=311,328,3,3;ANN=A|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20415G>A|p.Arg6805Arg|20415/21290|20415/21290|6805/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20712 . AAG A 77.0 PASS DP=607;AF=0.006590;SB=0;DP4=288,315,2,2;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20449_20450delGA|p.Glu6817fs|20449/21290|20449/21290|6817/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 20724 . AG A 77.0 PASS DP=592;AF=0.006757;SB=0;DP4=281,307,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant&stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20460delG|p.Ser6822fs|20460/21290|20460/21290|6820/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20874 . TGG T 51.0 PASS DP=864;AF=0.003472;SB=0;DP4=524,337,2,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20610_20611delGG|p.Val6871fs|20610/21290|20610/21290|6870/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20964 . CT C 64.0 PASS DP=1344;AF=0.002976;SB=0;DP4=678,670,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20702delT|p.Leu6901fs|20702/21290|20702/21290|6901/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&INFO_REALIGN_3_PRIME -MN908947.3 20995 . G T 73.0 PASS DP=1318;AF=0.004552;SB=0;DP4=658,654,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20730G>T|p.Leu6910Phe|20730/21290|20730/21290|6910/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21003 . TG T 64.0 PASS DP=1324;AF=0.003021;SB=0;DP4=659,661,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20739delG|p.Gln6914fs|20739/21290|20739/21290|6913/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21031 . G T 74.0 PASS DP=1212;AF=0.004950;SB=0;DP4=602,602,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20766G>T|p.Gly6922Gly|20766/21290|20766/21290|6922/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21650 . A C 61.0 PASS DP=357;AF=0.011204;SB=0;DP4=154,199,2,2;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.88A>C|p.Asn30His|88/3822|88/3822|30/1273|| -MN908947.3 21667 . T G 95.0 PASS DP=364;AF=0.030220;SB=4;DP4=162,191,7,4;ANN=G|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.105T>G|p.Gly35Gly|105/3822|105/3822|35/1273|| -MN908947.3 21764 . ATACATG A 16780.0 PASS DP=449;AF=0.986637;SB=0;DP4=2,2,244,199;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.204_209delACATGT|p.His69_Val70del|204/3822|204/3822|68/1273||INFO_REALIGN_3_PRIME -MN908947.3 21990 . TTTA T 8304.0 PASS DP=243;AF=0.876543;SB=7;DP4=12,21,107,106;INDEL;HRUN=3;ANN=T|disruptive_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.432_434delTTA|p.Tyr145del|432/3822|432/3822|144/1273||INFO_REALIGN_3_PRIME -MN908947.3 22283 . T C 69.0 PASS DP=273;AF=0.014652;SB=1;DP4=101,168,2,2;ANN=C|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.721T>C|p.Leu241Leu|721/3822|721/3822|241/1273|| -MN908947.3 22643 . TG T 80.0 PASS DP=510;AF=0.007843;SB=0;DP4=272,234,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1082delG|p.Cys361fs|1082/3822|1082/3822|361/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 23063 . A T 10180.0 PASS DP=264;AF=0.996212;SB=0;DP4=0,0,132,132;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| -MN908947.3 23271 . C A 44093.0 PASS DP=1158;AF=0.996546;SB=0;DP4=1,1,591,563;ANN=A|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| -MN908947.3 23294 . G T 101.0 PASS DP=1302;AF=0.006144;SB=0;DP4=658,634,4,4;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1732G>T|p.Asp578Tyr|1732/3822|1732/3822|578/1273|| -MN908947.3 23403 . A G 42730.0 PASS DP=1137;AF=0.995602;SB=0;DP4=0,0,496,637;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| -MN908947.3 23547 . G C 101.0 PASS DP=821;AF=0.008526;SB=0;DP4=445,365,4,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1985G>C|p.Cys662Ser|1985/3822|1985/3822|662/1273|| -MN908947.3 23604 . C A 37398.0 PASS DP=988;AF=0.995951;SB=0;DP4=0,0,485,503;ANN=A|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2042C>A|p.Pro681His|2042/3822|2042/3822|681/1273|| -MN908947.3 23709 . C T 21391.0 PASS DP=553;AF=1.000000;SB=0;DP4=0,0,96,457;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2147C>T|p.Thr716Ile|2147/3822|2147/3822|716/1273|| -MN908947.3 23803 . TG T 116.0 PASS DP=273;AF=0.018315;SB=0;DP4=102,166,2,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2242delG|p.Glu748fs|2242/3822|2242/3822|748/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24197 . G T 92.0 PASS DP=542;AF=0.011070;SB=1;DP4=296,240,4,2;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2635G>T|p.Ala879Ser|2635/3822|2635/3822|879/1273|| -MN908947.3 24506 . T G 32597.0 PASS DP=849;AF=1.000000;SB=0;DP4=0,0,471,378;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| -MN908947.3 24672 . CA C 60.0 PASS DP=907;AF=0.004410;SB=0;DP4=396,507,2,2;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3115delA|p.Arg1039fs|3115/3822|3115/3822|1039/1273||INFO_REALIGN_3_PRIME;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24821 . G C 76.0 PASS DP=1161;AF=0.005168;SB=0;DP4=594,561,3,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3259G>C|p.Ala1087Pro|3259/3822|3259/3822|1087/1273|| -MN908947.3 24914 . G C 46451.0 PASS DP=1236;AF=1.000000;SB=0;DP4=0,0,611,625;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| -MN908947.3 24931 . TG T 66.0 PASS DP=1143;AF=0.003500;SB=0;DP4=559,580,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3371delG|p.Gly1124fs|3371/3822|3371/3822|1124/1273||INFO_REALIGN_3_PRIME;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24959 . G T 80.0 PASS DP=963;AF=0.006231;SB=0;DP4=434,521,3,3;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3397G>T|p.Val1133Phe|3397/3822|3397/3822|1133/1273|| -MN908947.3 25186 . G C 74.0 PASS DP=1157;AF=0.005186;SB=0;DP4=574,577,3,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3624G>C|p.Gln1208His|3624/3822|3624/3822|1208/1273|| -MN908947.3 25301 . TG T 71.0 PASS DP=719;AF=0.005563;SB=0;DP4=304,412,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3740delG|p.Cys1247fs|3740/3822|3740/3822|1247/1273|| -MN908947.3 25314 . G T 81.0 PASS DP=707;AF=0.008487;SB=1;DP4=323,378,2,4;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3752G>T|p.Gly1251Val|3752/3822|3752/3822|1251/1273|| -MN908947.3 25317 . C G 84.0 PASS DP=697;AF=0.008608;SB=1;DP4=317,374,2,4;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3755C>G|p.Ser1252Cys|3755/3822|3755/3822|1252/1273|| -MN908947.3 25325 . A T 70.0 PASS DP=680;AF=0.007353;SB=7;DP4=307,368,4,1;ANN=T|stop_gained|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3763A>T|p.Lys1255*|3763/3822|3763/3822|1255/1273|| -MN908947.3 25608 . A C 71.0 PASS DP=439;AF=0.011390;SB=15;DP4=127,307,4,1;ANN=C|synonymous_variant|LOW|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.216A>C|p.Ala72Ala|216/828|216/828|72/275|| -MN908947.3 25628 . TTG T 58.0 PASS DP=466;AF=0.006438;SB=2;DP4=223,242,2,1;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.238_239delGT|p.Val80fs|238/828|238/828|80/275||INFO_REALIGN_3_PRIME;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 25629 . TG T 58.0 PASS DP=466;AF=0.006438;SB=0;DP4=223,242,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.238delG|p.Val80fs|238/828|238/828|80/275||;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 26157 . TGTTA T 68.0 PASS DP=1010;AF=0.003960;SB=0;DP4=501,510,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.766_769delGTTA|p.Val256fs|766/828|766/828|256/275||;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 26209 . G T 63.0 PASS DP=840;AF=0.005952;SB=0;DP4=363,472,2,3;ANN=T|missense_variant|MODERATE|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.817G>T|p.Val273Leu|817/828|817/828|273/275|| -MN908947.3 26261 . CG C 108.0 PASS DP=886;AF=0.006772;SB=3;DP4=470,410,2,4;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.19delG|p.Glu7fs|19/228|19/228|7/75||INFO_REALIGN_3_PRIME;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26354 . TTCG T 66.0 PASS DP=1142;AF=0.003503;SB=0;DP4=570,568,2,2;INDEL;HRUN=2;ANN=T|disruptive_inframe_deletion|MODERATE|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.111_113delTCG|p.Arg38del|111/228|111/228|37/75|| -MN908947.3 26366 . CG C 66.0 PASS DP=1197;AF=0.003342;SB=0;DP4=594,599,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.123delG|p.Tyr42fs|123/228|123/228|41/75||;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26367 . G T 136.0 PASS DP=1200;AF=0.008333;SB=0;DP4=590,596,5,5;ANN=T|synonymous_variant|LOW|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.123G>T|p.Ala41Ala|123/228|123/228|41/75|| -MN908947.3 26408 . CT C 59.0 PASS DP=1171;AF=0.003416;SB=0;DP4=571,596,2,2;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.169delT|p.Tyr57fs|169/228|169/228|57/75||INFO_REALIGN_3_PRIME;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26713 . GT G 133.0 PASS DP=1343;AF=0.005957;SB=0;DP4=691,649,4,4;INDEL;HRUN=4;ANN=G|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.195delT|p.Phe65fs|195/669|195/669|65/222||INFO_REALIGN_3_PRIME;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26720 . G A 127.0 PASS DP=1331;AF=0.007513;SB=0;DP4=673,646,5,5;ANN=A|synonymous_variant|LOW|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.198G>A|p.Val66Val|198/669|198/669|66/222|| -MN908947.3 26721 . CTT C 170.0 PASS DP=1321;AF=0.007570;SB=0;DP4=673,648,5,5;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.200_201delTT|p.Leu67fs|200/669|200/669|67/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26736 . AG A 64.0 PASS DP=1315;AF=0.003042;SB=0;DP4=666,645,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.215delG|p.Arg72fs|215/669|215/669|72/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26776 . CTTG C 65.0 PASS DP=1246;AF=0.003210;SB=0;DP4=598,651,2,2;INDEL;HRUN=2;ANN=C|conservative_inframe_deletion|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.256_258delTGT|p.Cys86del|256/669|256/669|86/222||INFO_REALIGN_3_PRIME -MN908947.3 26783 . TG T 99.0 PASS DP=1067;AF=0.005623;SB=1;DP4=469,636,3,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.262delG|p.Val88fs|262/669|262/669|88/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 27029 . TG T 51.0 PASS DP=855;AF=0.003509;SB=0;DP4=418,434,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.508delG|p.Val170fs|508/669|508/669|170/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 27052 . CTTA C 72.0 PASS DP=857;AF=0.004667;SB=0;DP4=414,439,2,2;INDEL;HRUN=2;ANN=C|disruptive_inframe_deletion|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.534_536delTTA|p.Tyr179del|534/669|534/669|178/222||INFO_REALIGN_3_PRIME -MN908947.3 27183 . G C 167.0 PASS DP=861;AF=0.012776;SB=2;DP4=512,337,8,3;ANN=C|missense_variant|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.661G>C|p.Val221Leu|661/669|661/669|221/222|| -MN908947.3 27194 . GACAACAGATGTTTCATCTCGTTGACTT G 69.0 PASS DP=951;AF=0.004206;SB=1;DP4=607,365,2,2;INDEL;HRUN=1;ANN=G|frameshift_variant&start_lost|HIGH|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.-7_20delACAACAGATGTTTCATCTCGTTGACTT|p.Met1fs||1/186|1/61||;LOF=(ORF6|gene-GU280_gp06|1|1.00) -MN908947.3 27281 . G C 67.0 PASS DP=1702;AF=0.003525;SB=0;DP4=847,839,3,3;ANN=C|missense_variant|MODERATE|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.80G>C|p.Trp27Ser|80/186|80/186|27/61|| -MN908947.3 27366 . G T 94.0 PASS DP=1764;AF=0.004535;SB=0;DP4=869,885,4,4;ANN=T|missense_variant|MODERATE|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.165G>T|p.Glu55Asp|165/186|165/186|55/61|| -MN908947.3 27394 . ATG A 78.0 PASS DP=1653;AF=0.003025;SB=1;DP4=804,845,3,2;INDEL;HRUN=1;ANN=A|frameshift_variant&start_lost|HIGH|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.2_3delTG|p.Met1fs|2/366|2/366|1/121||;LOF=(ORF7a|gene-GU280_gp07|1|1.00) -MN908947.3 27476 . C T 102.0 PASS DP=683;AF=0.013177;SB=0;DP4=232,442,3,6;ANN=T|missense_variant|MODERATE|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.83C>T|p.Thr28Ile|83/366|83/366|28/121|| -MN908947.3 27494 . C T 137.0 PASS DP=495;AF=0.018182;SB=1;DP4=158,328,2,7;ANN=T|missense_variant|MODERATE|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.101C>T|p.Pro34Leu|101/366|101/366|34/121|| -MN908947.3 27972 . C T 18460.0 PASS DP=481;AF=1.000000;SB=0;DP4=0,0,245,236;ANN=T|stop_gained|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| -MN908947.3 28000 . CG C 81.0 PASS DP=482;AF=0.008299;SB=0;DP4=242,236,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.108delG|p.Cys37fs|108/366|108/366|36/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28048 . G T 15365.0 PASS DP=404;AF=0.995049;SB=0;DP4=0,0,196,208;ANN=T|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| -MN908947.3 28073 . G C 64.0 PASS DP=322;AF=0.012422;SB=0;DP4=131,187,2,2;ANN=C|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.180G>C|p.Leu60Phe|180/366|180/366|60/121|| -MN908947.3 28111 . A G 18931.0 PASS DP=519;AF=0.996146;SB=0;DP4=0,0,321,198;ANN=G|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| -MN908947.3 28196 . TTG T 50.0 PASS DP=936;AF=0.003205;SB=0;DP4=527,406,2,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.305_306delGT|p.Cys102fs|305/366|305/366|102/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28197 . TG T 69.0 PASS DP=950;AF=0.004211;SB=0;DP4=530,416,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.305delG|p.Cys102fs|305/366|305/366|102/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28207 . ATG A 68.0 PASS DP=1036;AF=0.003861;SB=0;DP4=542,490,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.315_316delTG|p.Tyr105fs|315/366|315/366|105/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28214 . C CT 60.0 PASS DP=1052;AF=0.003802;SB=0;DP4=546,505,2,2;INDEL;HRUN=5;ANN=CT|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.326dupT|p.Leu109fs|327/366|327/366|109/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28270 . TA T 22586.0 PASS DP=1102;AF=0.956443;SB=0;DP4=26,24,532,522;INDEL;HRUN=4 -MN908947.3 28280 . G C 22789.0 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520;ANN=C|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.7G>C|p.Asp3His|7/1260|7/1260|3/419|| -MN908947.3 28281 . A T 22802.0 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520;ANN=T|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.8A>T|p.Asp3Val|8/1260|8/1260|3/419|| -MN908947.3 28282 . T A 22760.0 PASS DP=1052;AF=0.997148;SB=0;DP4=1,1,530,520;ANN=A|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.9T>A|p.Asp3Glu|9/1260|9/1260|3/419|| -MN908947.3 28324 . TG T 67.0 PASS DP=1086;AF=0.003683;SB=0;DP4=535,548,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.53delG|p.Gly18fs|53/1260|53/1260|18/419||INFO_REALIGN_3_PRIME -MN908947.3 28406 . T TA 168.0 PASS DP=590;AF=0.013559;SB=1;DP4=198,388,2,6;INDEL;HRUN=3;ANN=TA|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.133_134insA|p.Leu45fs|134/1260|134/1260|45/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 28881 . G A 21462.0 PASS DP=563;AF=0.996448;SB=0;DP4=1,1,290,271;ANN=A|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.608G>A|p.Arg203Lys|608/1260|608/1260|203/419|| -MN908947.3 28882 . G A 20841.0 PASS DP=561;AF=0.991087;SB=0;DP4=1,1,288,271;ANN=A|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.609G>A|p.Arg203Arg|609/1260|609/1260|203/419|| -MN908947.3 28883 . G C 21251.0 PASS DP=562;AF=0.994662;SB=0;DP4=1,1,287,272;ANN=C|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.610G>C|p.Gly204Arg|610/1260|610/1260|204/419|| -MN908947.3 28886 . A G 83.0 PASS DP=564;AF=0.010638;SB=0;DP4=286,272,3,3;ANN=G|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.613A>G|p.Thr205Ala|613/1260|613/1260|205/419|| -MN908947.3 28977 . C T 9754.0 PASS DP=254;AF=1.000000;SB=0;DP4=0,0,26,228;ANN=T|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| -MN908947.3 29104 . TG T 76.0 PASS DP=634;AF=0.006309;SB=1;DP4=356,274,3,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.833delG|p.Gly278fs|833/1260|833/1260|278/419||INFO_REALIGN_3_PRIME;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29144 . C T 731.0 PASS DP=763;AF=0.045872;SB=3;DP4=382,346,16,19;ANN=T|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.871C>T|p.Leu291Leu|871/1260|871/1260|291/419|| -MN908947.3 29178 . CG C 74.0 PASS DP=753;AF=0.005312;SB=0;DP4=391,358,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.906delG|p.Gln303fs|906/1260|906/1260|302/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29281 . C T 116.0 PASS DP=475;AF=0.014737;SB=1;DP4=198,270,2,5;ANN=T|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.1008C>T|p.Ala336Ala|1008/1260|1008/1260|336/419|| -MN908947.3 29353 . C CA 52.0 PASS DP=605;AF=0.004959;SB=0;DP4=338,279,2,1;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.1084dupA|p.Thr362fs|1085/1260|1085/1260|362/419||INFO_REALIGN_3_PRIME;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29543 . G T 65.0 PASS DP=1553;AF=0.005151;SB=0;DP4=814,729,4,4 -MN908947.3 29642 . C T 169.0 PASS DP=1375;AF=0.008727;SB=6;DP4=605,756,3,9;ANN=T|stop_gained|HIGH|ORF10|gene-GU280_gp11|transcript|TRANSCRIPT_gene-GU280_gp11|protein_coding|1/1|c.85C>T|p.Gln29*|85/117|85/117|29/38|| -MN908947.3 29645 . G T 101.0 PASS DP=1352;AF=0.005917;SB=0;DP4=600,742,4,4;ANN=T|missense_variant|MODERATE|ORF10|gene-GU280_gp11|transcript|TRANSCRIPT_gene-GU280_gp11|protein_coding|1/1|c.88G>T|p.Val30Leu|88/117|88/117|30/38|| -MN908947.3 29736 . G T 80.0 PASS DP=868;AF=0.006912;SB=0;DP4=419,443,3,3 -MN908947.3 29748 . TACG T 51.0 PASS DP=842;AF=0.003563;SB=2;DP4=401,441,2,1;INDEL;HRUN=1 diff --git a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated2.vcf b/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated2.vcf deleted file mode 100644 index 5c682b7..0000000 --- a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.annotated2.vcf +++ /dev/null @@ -1,278 +0,0 @@ -##fileformat=VCFv4.0 -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5229917/ERR5229917.preprocessed.lofreq.vcf ERR5229917/ERR5229917.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" -##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-intergenic -no-intron -noShiftHgvs SARS-COV2 ERR5229917/ERR5229917.preprocessed.lofreq.vcf " -##INFO= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 173 . CG C 72.0 PASS DP=760;AF=0.005263;SB=0;DP4=406,352,2,2;INDEL;HRUN=1 -MN908947.3 241 . C T 29888.0 PASS DP=800;AF=0.995000;SB=0;DP4=1,1,390,406 -MN908947.3 283 . TG T 74.0 PASS DP=726;AF=0.005510;SB=0;DP4=337,385,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19delG|p.Gly7fs|19/21290|19/21290|7/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 336 . G A 136.0 PASS DP=610;AF=0.018033;SB=1;DP4=251,345,4,7;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.71G>A|p.Arg24His|71/21290|71/21290|24/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 370 . G C 63.0 PASS DP=662;AF=0.007553;SB=6;DP4=314,341,4,1;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.105G>C|p.Val35Val|105/21290|105/21290|35/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 376 . G T 61.0 PASS DP=671;AF=0.007452;SB=0;DP4=347,317,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.111G>T|p.Glu37Asp|111/21290|111/21290|37/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 377 . G GC 52.0 PASS DP=659;AF=0.004552;SB=0;DP4=346,322,2,1;INDEL;HRUN=1;ANN=GC|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.112_113insC|p.Val38fs|113/21290|113/21290|38/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 419 . G T 72.0 PASS DP=634;AF=0.007886;SB=0;DP4=379,250,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.154G>T|p.Gly52Cys|154/21290|154/21290|52/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 509 . GGTCATGTTATGGTT G 70.0 PASS DP=914;AF=0.004376;SB=0;DP4=458,452,2,2;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.245_258delGTCATGTTATGGTT|p.His83fs|245/21290|245/21290|82/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 534 . CAG C 71.0 PASS DP=902;AF=0.004435;SB=0;DP4=447,457,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.270_271delAG|p.Glu91fs|270/21290|270/21290|90/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 536 . G T 83.0 PASS DP=901;AF=0.006659;SB=0;DP4=439,450,3,3;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.271G>T|p.Glu91*|271/21290|271/21290|91/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 738 . AAG A 97.0 PASS DP=712;AF=0.007022;SB=3;DP4=404,303,4,1;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.474_475delAG|p.Glu159fs|474/21290|474/21290|158/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 794 . CT C 110.0 PASS DP=1051;AF=0.005709;SB=0;DP4=534,513,3,3;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.530delT|p.Asn178fs|530/21290|530/21290|177/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 884 . CG C 68.0 PASS DP=1049;AF=0.003813;SB=0;DP4=515,536,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.620delG|p.Arg207fs|620/21290|620/21290|207/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 899 . T A 136.0 PASS DP=1023;AF=0.009775;SB=1;DP4=487,526,4,6;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.634T>A|p.Ser212Thr|634/21290|634/21290|212/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 900 . C A 134.0 PASS DP=1018;AF=0.009823;SB=1;DP4=480,528,4,6;ANN=A|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.635C>A|p.Ser212*|635/21290|635/21290|212/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 913 . C T 35817.0 PASS DP=931;AF=1.000000;SB=0;DP4=0,0,417,514;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.648C>T|p.Ser216Ser|648/21290|648/21290|216/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 931 . TG T 156.0 PASS DP=844;AF=0.009479;SB=0;DP4=354,492,3,5;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.667delG|p.Asp223fs|667/21290|667/21290|223/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1027 . T C 81.0 PASS DP=544;AF=0.011029;SB=1;DP4=320,218,3,3;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.762T>C|p.Pro254Pro|762/21290|762/21290|254/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1104 . T C 127.0 PASS DP=708;AF=0.011299;SB=0;DP4=346,354,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.839T>C|p.Ile280Thr|839/21290|839/21290|280/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1216 . T G 305.0 PASS DP=537;AF=0.029795;SB=3;DP4=222,299,5,11;ANN=G|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.951T>G|p.Leu317Leu|951/21290|951/21290|317/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1302 . C T 62.0 PASS DP=350;AF=0.011429;SB=0;DP4=155,191,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1037C>T|p.Thr346Ile|1037/21290|1037/21290|346/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1406 . G T 61.0 PASS DP=445;AF=0.008989;SB=0;DP4=222,216,2,2;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1141G>T|p.Glu381*|1141/21290|1141/21290|381/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 1720 . TG T 54.0 PASS DP=596;AF=0.005034;SB=0;DP4=302,289,2,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1456delG|p.Ala486fs|1456/21290|1456/21290|486/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 1813 . T TA 112.0 PASS DP=593;AF=0.013491;SB=0;DP4=290,295,4,4;INDEL;HRUN=6;ANN=TA|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1548_1549insA|p.Gly519fs|1549/21290|1549/21290|517/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2157 . T C 61.0 PASS DP=341;AF=0.011730;SB=0;DP4=141,196,2,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1892T>C|p.Leu631Pro|1892/21290|1892/21290|631/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2229 . G T 63.0 PASS DP=287;AF=0.013937;SB=0;DP4=155,128,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.1964G>T|p.Cys655Phe|1964/21290|1964/21290|655/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2365 . TA T 55.0 PASS DP=609;AF=0.004926;SB=2;DP4=313,295,1,2;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2101delA|p.Ala702fs|2101/21290|2101/21290|701/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2403 . CA C 82.0 PASS DP=672;AF=0.008929;SB=0;DP4=337,329,3,3;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2139delA|p.Lys714fs|2139/21290|2139/21290|713/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2557 . AC A 80.0 PASS DP=511;AF=0.007828;SB=0;DP4=265,242,2,2;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2293delC|p.Pro765fs|2293/21290|2293/21290|765/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2644 . C T 100.0 PASS DP=855;AF=0.008187;SB=0;DP4=446,402,4,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2379C>T|p.Ile793Ile|2379/21290|2379/21290|793/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2714 . G T 77.0 PASS DP=981;AF=0.006116;SB=0;DP4=488,487,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2449G>T|p.Gly817Cys|2449/21290|2449/21290|817/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 2777 . AGT A 74.0 PASS DP=754;AF=0.005305;SB=0;DP4=327,427,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2513_2514delGT|p.Val839fs|2513/21290|2513/21290|838/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 2889 . TG T 86.0 PASS DP=704;AF=0.008523;SB=10;DP4=394,304,1,5;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2625delG|p.Ala876fs|2625/21290|2625/21290|875/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 3037 . C T 31757.0 PASS DP=825;AF=1.000000;SB=0;DP4=0,0,371,454;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2772C>T|p.Phe924Phe|2772/21290|2772/21290|924/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3177 . C T 19987.0 PASS DP=545;AF=0.990826;SB=0;DP4=1,1,304,239;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2912C>T|p.Pro971Leu|2912/21290|2912/21290|971/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3239 . G T 63.0 PASS DP=872;AF=0.005734;SB=1;DP4=509,358,4,1;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2974G>T|p.Asp992Tyr|2974/21290|2974/21290|992/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3250 . G C 79.0 PASS DP=967;AF=0.006205;SB=0;DP4=535,422,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2985G>C|p.Glu995Asp|2985/21290|2985/21290|995/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3267 . C T 43568.0 PASS DP=1150;AF=0.998261;SB=0;DP4=0,0,590,560;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3002C>T|p.Thr1001Ile|3002/21290|3002/21290|1001/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3549 . G C 63.0 PASS DP=334;AF=0.011976;SB=0;DP4=187,143,2,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3284G>C|p.Gly1095Ala|3284/21290|3284/21290|1095/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3557 . A G 64.0 PASS DP=363;AF=0.011019;SB=0;DP4=197,162,2,2;ANN=G|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3292A>G|p.Lys1098Glu|3292/21290|3292/21290|1098/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3768 . C T 68.0 PASS DP=221;AF=0.018100;SB=2;DP4=73,144,2,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3503C>T|p.Thr1168Ile|3503/21290|3503/21290|1168/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 3802 . TA T 56.0 PASS DP=359;AF=0.008357;SB=0;DP4=238,127,2,1;INDEL;HRUN=5;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3538delA|p.Asn1181fs|3538/21290|3538/21290|1180/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 3837 . TG T 84.0 PASS DP=405;AF=0.009877;SB=2;DP4=270,131,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3573delG|p.Glu1192fs|3573/21290|3573/21290|1191/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4147 . TG T 73.0 PASS DP=762;AF=0.005249;SB=2;DP4=412,351,3,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3883delG|p.Val1295fs|3883/21290|3883/21290|1295/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4189 . CA C 70.0 PASS DP=907;AF=0.004410;SB=0;DP4=469,435,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3925delA|p.Thr1309fs|3925/21290|3925/21290|1309/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4254 . CG C 69.0 PASS DP=969;AF=0.004128;SB=0;DP4=495,472,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.3990delG|p.Gly1331fs|3990/21290|3990/21290|1330/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4290 . CA C 71.0 PASS DP=895;AF=0.004469;SB=0;DP4=443,448,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4026delA|p.Lys1343fs|4026/21290|4026/21290|1342/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 4398 . TG T 70.0 PASS DP=942;AF=0.004246;SB=0;DP4=471,468,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.4134delG|p.Met1378fs|4134/21290|4134/21290|1378/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5388 . C A 42501.0 PASS DP=1107;AF=1.000000;SB=0;DP4=0,0,559,548;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5123C>A|p.Ala1708Asp|5123/21290|5123/21290|1708/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 5530 . TG T 109.0 PASS DP=1099;AF=0.005460;SB=1;DP4=487,606,2,4;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5266delG|p.Gly1756fs|5266/21290|5266/21290|1756/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5706 . ATG A 61.0 PASS DP=1419;AF=0.002819;SB=4;DP4=716,700,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5442_5443delTG|p.Tyr1814fs|5442/21290|5442/21290|1814/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5744 . T C 66.0 PASS DP=1517;AF=0.003955;SB=0;DP4=764,745,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5479T>C|p.Tyr1827His|5479/21290|5479/21290|1827/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 5770 . CTA C 62.0 PASS DP=1503;AF=0.002661;SB=0;DP4=772,737,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5506_5507delTA|p.Tyr1836fs|5506/21290|5506/21290|1836/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 5986 . C T 21855.0 PASS DP=582;AF=1.000000;SB=0;DP4=0,0,327,255;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5721C>T|p.Phe1907Phe|5721/21290|5721/21290|1907/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6180 . AT A 62.0 PASS DP=593;AF=0.006745;SB=0;DP4=271,319,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5916delT|p.Tyr1972fs|5916/21290|5916/21290|1972/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6241 . G C 82.0 PASS DP=1297;AF=0.005397;SB=0;DP4=758,532,4,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.5976G>C|p.Trp1992Cys|5976/21290|5976/21290|1992/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6330 . C CA 58.0 PASS DP=1890;AF=0.002116;SB=0;DP4=957,929,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6065_6066insA|p.Asn2023fs|6066/21290|6066/21290|2022/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6388 . C T 64.0 PASS DP=1851;AF=0.003241;SB=0;DP4=922,923,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6123C>T|p.Cys2041Cys|6123/21290|6123/21290|2041/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 6437 . CAG C 63.0 PASS DP=1422;AF=0.002813;SB=0;DP4=591,843,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6173_6174delAG|p.Lys2059fs|6173/21290|6173/21290|2058/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6445 . CG C 64.0 PASS DP=1323;AF=0.003023;SB=1;DP4=531,801,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6181delG|p.Val2061fs|6181/21290|6181/21290|2061/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6655 . TAATAGTGTCCCTTGGGATACTATAGCTA T 152.0 PASS DP=1155;AF=0.006926;SB=0;DP4=572,577,4,4;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6391_6418delAATAGTGTCCCTTGGGATACTATAGCTA|p.Asn2131fs|6391/21290|6391/21290|2131/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6696 . C CT 103.0 PASS DP=1114;AF=0.005386;SB=3;DP4=563,558,2,4;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6431_6432insT|p.Leu2146fs|6432/21290|6432/21290|2144/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 6954 . T C 28841.0 PASS DP=750;AF=0.998667;SB=0;DP4=0,0,358,392;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.6689T>C|p.Ile2230Thr|6689/21290|6689/21290|2230/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 7462 . TG T 108.0 PASS DP=986;AF=0.006085;SB=0;DP4=480,502,3,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7198delG|p.Val2400fs|7198/21290|7198/21290|2400/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 7640 . TG T 57.0 PASS DP=516;AF=0.005814;SB=0;DP4=216,297,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7376delG|p.Cys2459fs|7376/21290|7376/21290|2459/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 7948 . CAG C 77.0 PASS DP=571;AF=0.007005;SB=2;DP4=207,403,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7684_7685delAG|p.Gln2563fs|7684/21290|7684/21290|2562/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8128 . AAAG A 58.0 PASS DP=1839;AF=0.002175;SB=0;DP4=919,918,2,2;INDEL;HRUN=3;ANN=A|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7864_7866delAAG|p.Lys2622del|7864/21290|7864/21290|2622/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 8133 . ATG A 58.0 PASS DP=1862;AF=0.002148;SB=0;DP4=932,930,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7869_7870delTG|p.Ser2625fs|7869/21290|7869/21290|2623/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8187 . T C 121.0 PASS DP=1758;AF=0.005688;SB=0;DP4=855,891,5,5;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.7922T>C|p.Phe2641Ser|7922/21290|7922/21290|2641/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 8345 . TG T 55.0 PASS DP=484;AF=0.006198;SB=2;DP4=330,151,3,0;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8081delG|p.Cys2694fs|8081/21290|8081/21290|2694/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8430 . CTG C 73.0 PASS DP=799;AF=0.005006;SB=0;DP4=397,398,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8166_8167delTG|p.Glu2723fs|8166/21290|8166/21290|2722/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 8945 . AAC A 57.0 PASS DP=530;AF=0.005660;SB=2;DP4=253,278,2,1;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8681_8682delAC|p.Ile2895fs|8681/21290|8681/21290|2894/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9250 . TG T 93.0 PASS DP=729;AF=0.008230;SB=0;DP4=424,301,4,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.8986delG|p.Val2996fs|8986/21290|8986/21290|2996/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9314 . G T 75.0 PASS DP=1245;AF=0.005622;SB=0;DP4=667,568,4,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9049G>T|p.Val3017Phe|9049/21290|9049/21290|3017/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 9319 . CTG C 65.0 PASS DP=1275;AF=0.003137;SB=0;DP4=678,595,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9055_9056delTG|p.Cys3019fs|9055/21290|9055/21290|3019/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9331 . TG T 53.0 PASS DP=1434;AF=0.002789;SB=0;DP4=732,707,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9067delG|p.Ala3023fs|9067/21290|9067/21290|3023/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9583 . TG T 69.0 PASS DP=991;AF=0.004036;SB=0;DP4=569,418,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9319delG|p.Val3107fs|9319/21290|9319/21290|3107/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9790 . TG T 69.0 PASS DP=617;AF=0.006483;SB=2;DP4=219,396,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9526delG|p.Glu3176fs|9526/21290|9526/21290|3176/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 9801 . CG C 127.0 PASS DP=663;AF=0.010558;SB=0;DP4=254,404,3,4;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.9537delG|p.Leu3180fs|9537/21290|9537/21290|3179/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10426 . TG T 56.0 PASS DP=1096;AF=0.003650;SB=2;DP4=567,527,3,1;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10162delG|p.Val3388fs|10162/21290|10162/21290|3388/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10427 . G T 80.0 PASS DP=1116;AF=0.006272;SB=0;DP4=578,527,4,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10162G>T|p.Val3388Phe|10162/21290|10162/21290|3388/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 10527 . CT C 91.0 PASS DP=1435;AF=0.004181;SB=0;DP4=737,694,3,3;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10263delT|p.Cys3423fs|10263/21290|10263/21290|3421/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10625 . GCA G 64.0 PASS DP=1358;AF=0.002946;SB=0;DP4=658,711,2,2;INDEL;HRUN=1;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10361_10362delCA|p.Gln3455fs|10361/21290|10361/21290|3454/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 10776 . C T 66.0 PASS DP=767;AF=0.006519;SB=3;DP4=442,320,4,1;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10511C>T|p.Pro3504Leu|10511/21290|10511/21290|3504/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 10880 . ATG A 69.0 PASS DP=995;AF=0.004020;SB=0;DP4=478,513,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10616_10617delTG|p.Met3539fs|10616/21290|10616/21290|3539/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11028 . T C 101.0 PASS DP=696;AF=0.010057;SB=3;DP4=366,322,5,2;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10763T>C|p.Leu3588Ser|10763/21290|10763/21290|3588/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11107 . TG T 82.0 PASS DP=1407;AF=0.003554;SB=0;DP4=790,612,3,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10843delG|p.Ala3615fs|10843/21290|10843/21290|3615/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11121 . T C 75.0 PASS DP=1745;AF=0.004011;SB=0;DP4=920,814,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10856T>C|p.Ile3619Thr|10856/21290|10856/21290|3619/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11138 . G T 68.0 PASS DP=1893;AF=0.004226;SB=0;DP4=945,936,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10873G>T|p.Ala3625Ser|10873/21290|10873/21290|3625/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11145 . TG T 58.0 PASS DP=1923;AF=0.002080;SB=0;DP4=962,957,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10881delG|p.Met3627fs|10881/21290|10881/21290|3627/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11175 . G GT 57.0 PASS DP=2019;AF=0.001981;SB=0;DP4=1002,1013,2,2;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10910_10911insT|p.Leu3638fs|10911/21290|10911/21290|3637/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11236 . TAG T 57.0 PASS DP=1972;AF=0.002028;SB=0;DP4=969,999,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.10972_10973delAG|p.Ser3658fs|10972/21290|10972/21290|3658/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11287 . GTCTGGTTTT G 45483.0 PASS DP=1355;AF=0.996310;SB=71;DP4=69,33,541,809;INDEL;HRUN=1;ANN=G|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11023_11031delTCTGGTTTT|p.Ser3675_Phe3677del|11023/21290|11023/21290|3675/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 11482 . TG T 67.0 PASS DP=1097;AF=0.003646;SB=0;DP4=572,521,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11218delG|p.Val3740fs|11218/21290|11218/21290|3740/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11615 . TG T 83.0 PASS DP=1330;AF=0.003759;SB=0;DP4=747,579,3,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11351delG|p.Cys3784fs|11351/21290|11351/21290|3784/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11693 . GT G 62.0 PASS DP=1515;AF=0.002640;SB=0;DP4=757,770,2,2;INDEL;HRUN=3;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11429delT|p.Tyr3811fs|11429/21290|11429/21290|3810/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11722 . G GT 80.0 PASS DP=1580;AF=0.003165;SB=1;DP4=775,805,3,2;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11457_11458insT|p.Arg3821fs|11458/21290|11458/21290|3820/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11741 . CAG C 61.0 PASS DP=1546;AF=0.002587;SB=0;DP4=756,791,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11477_11478delAG|p.Gln3826fs|11477/21290|11477/21290|3826/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 11750 . C T 229.0 PASS DP=1577;AF=0.010146;SB=0;DP4=757,803,8,8;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11485C>T|p.Leu3829Phe|11485/21290|11485/21290|3829/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12233 . G A 71.0 PASS DP=1396;AF=0.004298;SB=0;DP4=672,718,3,3;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.11968G>A|p.Glu3990Lys|11968/21290|11968/21290|3990/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12333 . CA C 60.0 PASS DP=1311;AF=0.003051;SB=0;DP4=640,669,2,2;INDEL;HRUN=4;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12069delA|p.Val4025fs|12069/21290|12069/21290|4023/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12396 . C T 248.0 PASS DP=971;AF=0.015448;SB=2;DP4=392,564,5,10;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12131C>T|p.Ala4044Val|12131/21290|12131/21290|4044/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12400 . C T 97.0 PASS DP=952;AF=0.007353;SB=0;DP4=384,561,3,4;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12135C>T|p.Leu4045Leu|12135/21290|12135/21290|4045/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12459 . C T 61.0 PASS DP=877;AF=0.005701;SB=4;DP4=524,346,2,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12194C>T|p.Thr4065Ile|12194/21290|12194/21290|4065/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12602 . G A 71.0 PASS DP=1484;AF=0.004043;SB=0;DP4=767,711,3,3;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12337G>A|p.Glu4113Lys|12337/21290|12337/21290|4113/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 12646 . TG T 62.0 PASS DP=1468;AF=0.002725;SB=0;DP4=742,722,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12382delG|p.Val4128fs|12382/21290|12382/21290|4128/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12720 . TG T 69.0 PASS DP=968;AF=0.004132;SB=1;DP4=367,603,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12456delG|p.Met4152fs|12456/21290|12456/21290|4152/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 12911 . G A 429.0 PASS DP=1478;AF=0.017591;SB=4;DP4=729,723,16,10;ANN=A|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12646G>A|p.Val4216Ile|12646/21290|12646/21290|4216/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13115 . C T 64.0 PASS DP=1874;AF=0.003202;SB=0;DP4=1080,788,4,2;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12850C>T|p.Leu4284Leu|12850/21290|12850/21290|4284/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13141 . TAA T 72.0 PASS DP=2254;AF=0.002218;SB=1;DP4=1155,1098,2,3;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12877_12878delAA|p.Asn4293fs|12877/21290|12877/21290|4293/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13182 . A AG 53.0 PASS DP=2541;AF=0.001574;SB=0;DP4=1303,1234,2,2;INDEL;HRUN=2;ANN=AG|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.12917_12918insG|p.Ala4307fs|12918/21290|12918/21290|4306/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13345 . TG T 199.0 PASS DP=1348;AF=0.008160;SB=0;DP4=557,783,4,7;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13081delG|p.Val4361fs|13081/21290|13081/21290|4361/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13725 . TG T 50.0 PASS DP=802;AF=0.004988;SB=0;DP4=431,367,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13461delG|p.Leu4488fs|13461/21290|13461/21290|4487/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 13812 . G T 131.0 PASS DP=1017;AF=0.008850;SB=1;DP4=533,475,4,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13547G>T|p.Trp4516Leu|13547/21290|13547/21290|4516/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13978 . G C 149.0 PASS DP=763;AF=0.013106;SB=2;DP4=417,330,7,3;ANN=C|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13713G>C|p.Val4571Val|13713/21290|13713/21290|4571/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13978 . G T 78.0 PASS DP=763;AF=0.007864;SB=0;DP4=417,330,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13713G>T|p.Val4571Val|13713/21290|13713/21290|4571/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 13993 . G T 63.0 PASS DP=865;AF=0.005780;SB=1;DP4=470,388,2,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13728G>T|p.Lys4576Asn|13728/21290|13728/21290|4576/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14099 . G C 104.0 PASS DP=1246;AF=0.006421;SB=0;DP4=576,653,4,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.13834G>C|p.Val4612Leu|13834/21290|13834/21290|4612/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14408 . C T 42523.0 PASS DP=1109;AF=0.996393;SB=0;DP4=0,0,553,553;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14143C>T|p.Leu4715Leu|14143/21290|14143/21290|4715/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14571 . C T 126.0 PASS DP=691;AF=0.013025;SB=1;DP4=363,319,4,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14306C>T|p.Thr4769Ile|14306/21290|14306/21290|4769/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14676 . C T 49314.0 PASS DP=1416;AF=0.995763;SB=0;DP4=3,3,718,692;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14411C>T|p.Pro4804Leu|14411/21290|14411/21290|4804/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 14708 . CTG C 62.0 PASS DP=1464;AF=0.002732;SB=0;DP4=736,724,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14444_14445delTG|p.Cys4816fs|14444/21290|14444/21290|4815/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15202 . G T 82.0 PASS DP=711;AF=0.008439;SB=1;DP4=410,294,3,3;ANN=T|stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14937G>T|p.Ter4979Tyrext*?|14937/21290|14937/21290|4979/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15279 . C T 41710.0 PASS DP=1117;AF=0.998209;SB=0;DP4=0,0,615,502;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15014C>T|p.Thr5005Ile|15014/21290|15014/21290|5005/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15317 . T C 70.0 PASS DP=1380;AF=0.004348;SB=0;DP4=695,679,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15052T>C|p.Cys5018Arg|15052/21290|15052/21290|5018/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15441 . CATG C 88.0 PASS DP=1081;AF=0.004625;SB=0;DP4=470,607,2,3;INDEL;HRUN=1;ANN=C|disruptive_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15177_15179delATG|p.Cys5060del|15177/21290|15177/21290|5059/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 15443 . TG T 88.0 PASS DP=1062;AF=0.004708;SB=0;DP4=463,601,2,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15179delG|p.Cys5060fs|15179/21290|15179/21290|5060/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15960 . CG C 61.0 PASS DP=1602;AF=0.002497;SB=0;DP4=809,791,2,2;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15696delG|p.Ala5233fs|15696/21290|15696/21290|5232/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 15983 . TA T 53.0 PASS DP=1662;AF=0.002407;SB=0;DP4=824,834,2,2;INDEL;HRUN=5;ANN=T|frameshift_variant&stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15719delA|p.Lys5241fs|15719/21290|15719/21290|5240/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16072 . G T 67.0 PASS DP=1609;AF=0.003729;SB=0;DP4=772,829,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15807G>T|p.Met5269Ile|15807/21290|15807/21290|5269/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16074 . TG T 140.0 PASS DP=1578;AF=0.005070;SB=0;DP4=758,814,4,4;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15810delG|p.Met5271fs|15810/21290|15810/21290|5270/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16111 . C T 69.0 PASS DP=1218;AF=0.004926;SB=1;DP4=478,734,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15846C>T|p.Ser5282Ser|15846/21290|15846/21290|5282/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16114 . CATG C 86.0 PASS DP=1195;AF=0.004184;SB=0;DP4=472,721,2,3;INDEL;HRUN=1;ANN=C|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15850_15852delATG|p.Met5284del|15850/21290|15850/21290|5284/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16176 . T C 32264.0 PASS DP=875;AF=0.998857;SB=0;DP4=0,0,446,429;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15911T>C|p.Leu5304Pro|15911/21290|15911/21290|5304/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16191 . A T 82.0 PASS DP=676;AF=0.008876;SB=1;DP4=397,269,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.15926A>T|p.Asn5309Ile|15926/21290|15926/21290|5309/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16324 . TG T 67.0 PASS DP=1124;AF=0.003559;SB=0;DP4=518,602,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16060delG|p.Val5354fs|16060/21290|16060/21290|5354/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 16564 . G C 76.0 PASS DP=1179;AF=0.005089;SB=0;DP4=667,505,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16299G>C|p.Leu5433Phe|16299/21290|16299/21290|5433/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16647 . G C 68.0 PASS DP=1411;AF=0.004252;SB=0;DP4=709,696,3,3;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16382G>C|p.Arg5461Pro|16382/21290|16382/21290|5461/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16787 . G T 103.0 PASS DP=1082;AF=0.007394;SB=5;DP4=540,533,6,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16522G>T|p.Val5508Phe|16522/21290|16522/21290|5508/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 16852 . G T 131.0 PASS DP=1422;AF=0.007032;SB=0;DP4=826,586,6,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16587G>T|p.Met5529Ile|16587/21290|16587/21290|5529/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17178 . TG T 56.0 PASS DP=1685;AF=0.002374;SB=0;DP4=973,711,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16914delG|p.Met5639fs|16914/21290|16914/21290|5638/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17193 . G T 88.0 PASS DP=2032;AF=0.003937;SB=0;DP4=1046,976,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16928G>T|p.Arg5643Ile|16928/21290|16928/21290|5643/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17201 . TA T 53.0 PASS DP=2074;AF=0.001929;SB=0;DP4=1057,1015,2,2;INDEL;HRUN=4;ANN=T|frameshift_variant&stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16937delA|p.Asn5647fs|16937/21290|16937/21290|5646/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17247 . TG T 55.0 PASS DP=2191;AF=0.001826;SB=0;DP4=1102,1085,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.16983delG|p.Leu5662fs|16983/21290|16983/21290|5661/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17274 . CA C 67.0 PASS DP=2190;AF=0.002740;SB=0;DP4=1089,1098,3,3;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17010delA|p.Lys5671fs|17010/21290|17010/21290|5670/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17320 . G T 88.0 PASS DP=2074;AF=0.003857;SB=0;DP4=1027,1039,4,4;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17055G>T|p.Met5685Ile|17055/21290|17055/21290|5685/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17329 . G T 63.0 PASS DP=1902;AF=0.003155;SB=0;DP4=902,994,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17064G>T|p.Leu5688Leu|17064/21290|17064/21290|5688/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17338 . G T 61.0 PASS DP=1753;AF=0.003423;SB=0;DP4=789,957,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17073G>T|p.Gln5691His|17073/21290|17073/21290|5691/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17339 . CAG C 58.0 PASS DP=1715;AF=0.002332;SB=4;DP4=786,962,3,1;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17075_17076delAG|p.Gln5692fs|17075/21290|17075/21290|5692/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17359 . G T 70.0 PASS DP=1510;AF=0.003974;SB=0;DP4=645,859,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17094G>T|p.Met5698Ile|17094/21290|17094/21290|5698/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17569 . CCTG C 105.0 PASS DP=1273;AF=0.004713;SB=0;DP4=625,642,3,3;INDEL;HRUN=2;ANN=C|conservative_inframe_deletion|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17305_17307delCTG|p.Leu5769del|17305/21290|17305/21290|5769/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 17704 . AG A 53.0 PASS DP=735;AF=0.004082;SB=5;DP4=284,450,0,3;INDEL;HRUN=2;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17440delG|p.Gly5814fs|17440/21290|17440/21290|5814/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17727 . AG A 74.0 PASS DP=726;AF=0.005510;SB=1;DP4=312,411,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17463delG|p.Asn5822fs|17463/21290|17463/21290|5821/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 17749 . G T 84.0 PASS DP=622;AF=0.009646;SB=0;DP4=340,276,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.17484G>T|p.Leu5828Leu|17484/21290|17484/21290|5828/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18290 . G T 260.0 PASS DP=1061;AF=0.016023;SB=6;DP4=569,475,12,5;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18025G>T|p.Val6009Leu|18025/21290|18025/21290|6009/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18395 . CTG C 62.0 PASS DP=1423;AF=0.002811;SB=1;DP4=845,578,3,1;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18131_18132delTG|p.Tyr6045fs|18131/21290|18131/21290|6044/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 18443 . G T 95.0 PASS DP=1810;AF=0.004420;SB=0;DP4=927,873,4,4;ANN=T|stop_gained|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18178G>T|p.Glu6060*|18178/21290|18178/21290|6060/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18530 . TA T 61.0 PASS DP=1589;AF=0.002517;SB=0;DP4=737,861,2,2;INDEL;HRUN=3;ANN=T|frameshift_variant&stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18266delA|p.Arg6090fs|18266/21290|18266/21290|6089/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 18668 . G T 66.0 PASS DP=776;AF=0.006443;SB=0;DP4=468,302,3,2;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18403G>T|p.Val6135Leu|18403/21290|18403/21290|6135/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 18858 . TG T 68.0 PASS DP=1044;AF=0.003831;SB=0;DP4=494,551,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18594delG|p.Met6198fs|18594/21290|18594/21290|6198/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 19177 . G C 81.0 PASS DP=935;AF=0.006417;SB=0;DP4=376,552,2,4;ANN=C|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.18912G>C|p.Met6304Ile|18912/21290|18912/21290|6304/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19794 . G T 81.0 PASS DP=928;AF=0.006466;SB=0;DP4=459,463,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19529G>T|p.Gly6510Val|19529/21290|19529/21290|6510/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19860 . TG T 75.0 PASS DP=676;AF=0.005917;SB=1;DP4=277,395,1,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19596delG|p.Leu6533fs|19596/21290|19596/21290|6532/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 19937 . A G 142.0 PASS DP=414;AF=0.019324;SB=3;DP4=275,130,5,4;ANN=G|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19672A>G|p.Thr6558Ala|19672/21290|19672/21290|6558/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 19983 . C CT 82.0 PASS DP=517;AF=0.011605;SB=0;DP4=318,195,4,2;INDEL;HRUN=6;ANN=CT|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19718_19719insT|p.Leu6575fs|19719/21290|19719/21290|6573/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20029 . GC G 79.0 PASS DP=548;AF=0.007299;SB=0;DP4=320,225,2,2;INDEL;HRUN=3;ANN=G|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19765delC|p.Val6590fs|19765/21290|19765/21290|6589/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20133 . CG C 60.0 PASS DP=416;AF=0.007212;SB=0;DP4=159,254,1,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.19869delG|p.Ter6624fs|19869/21290|19869/21290|6623/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;LOF=(orf1ab|gene-GU280_gp01|1|1.00) -MN908947.3 20680 . G A 83.0 PASS DP=645;AF=0.009302;SB=0;DP4=311,328,3,3;ANN=A|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20415G>A|p.Arg6805Arg|20415/21290|20415/21290|6805/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20712 . AAG A 77.0 PASS DP=607;AF=0.006590;SB=0;DP4=288,315,2,2;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20448_20449delAG|p.Glu6817fs|20448/21290|20448/21290|6816/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20724 . AG A 77.0 PASS DP=592;AF=0.006757;SB=0;DP4=281,307,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant&stop_lost|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20460delG|p.Ser6822fs|20460/21290|20460/21290|6820/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20874 . TGG T 51.0 PASS DP=864;AF=0.003472;SB=0;DP4=524,337,2,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20610_20611delGG|p.Val6871fs|20610/21290|20610/21290|6870/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20964 . CT C 64.0 PASS DP=1344;AF=0.002976;SB=0;DP4=678,670,2,2;INDEL;HRUN=3;ANN=C|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20700delT|p.Leu6901fs|20700/21290|20700/21290|6900/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 20995 . G T 73.0 PASS DP=1318;AF=0.004552;SB=0;DP4=658,654,3,3;ANN=T|missense_variant|MODERATE|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20730G>T|p.Leu6910Phe|20730/21290|20730/21290|6910/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21003 . TG T 64.0 PASS DP=1324;AF=0.003021;SB=0;DP4=659,661,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20739delG|p.Gln6914fs|20739/21290|20739/21290|6913/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21031 . G T 74.0 PASS DP=1212;AF=0.004950;SB=0;DP4=602,602,3,3;ANN=T|synonymous_variant|LOW|orf1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.20766G>T|p.Gly6922Gly|20766/21290|20766/21290|6922/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS -MN908947.3 21650 . A C 61.0 PASS DP=357;AF=0.011204;SB=0;DP4=154,199,2,2;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.88A>C|p.Asn30His|88/3822|88/3822|30/1273|| -MN908947.3 21667 . T G 95.0 PASS DP=364;AF=0.030220;SB=4;DP4=162,191,7,4;ANN=G|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.105T>G|p.Gly35Gly|105/3822|105/3822|35/1273|| -MN908947.3 21764 . ATACATG A 16780.0 PASS DP=449;AF=0.986637;SB=0;DP4=2,2,244,199;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.203_208delTACATG|p.His69_Val70del|203/3822|203/3822|68/1273|| -MN908947.3 21990 . TTTA T 8304.0 PASS DP=243;AF=0.876543;SB=7;DP4=12,21,107,106;INDEL;HRUN=3;ANN=T|conservative_inframe_deletion|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.429_431delTTA|p.Tyr144del|429/3822|429/3822|143/1273|| -MN908947.3 22283 . T C 69.0 PASS DP=273;AF=0.014652;SB=1;DP4=101,168,2,2;ANN=C|synonymous_variant|LOW|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.721T>C|p.Leu241Leu|721/3822|721/3822|241/1273|| -MN908947.3 22643 . TG T 80.0 PASS DP=510;AF=0.007843;SB=0;DP4=272,234,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1082delG|p.Cys361fs|1082/3822|1082/3822|361/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 23063 . A T 10180.0 PASS DP=264;AF=0.996212;SB=0;DP4=0,0,132,132;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| -MN908947.3 23271 . C A 44093.0 PASS DP=1158;AF=0.996546;SB=0;DP4=1,1,591,563;ANN=A|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| -MN908947.3 23294 . G T 101.0 PASS DP=1302;AF=0.006144;SB=0;DP4=658,634,4,4;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1732G>T|p.Asp578Tyr|1732/3822|1732/3822|578/1273|| -MN908947.3 23403 . A G 42730.0 PASS DP=1137;AF=0.995602;SB=0;DP4=0,0,496,637;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| -MN908947.3 23547 . G C 101.0 PASS DP=821;AF=0.008526;SB=0;DP4=445,365,4,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1985G>C|p.Cys662Ser|1985/3822|1985/3822|662/1273|| -MN908947.3 23604 . C A 37398.0 PASS DP=988;AF=0.995951;SB=0;DP4=0,0,485,503;ANN=A|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2042C>A|p.Pro681His|2042/3822|2042/3822|681/1273|| -MN908947.3 23709 . C T 21391.0 PASS DP=553;AF=1.000000;SB=0;DP4=0,0,96,457;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2147C>T|p.Thr716Ile|2147/3822|2147/3822|716/1273|| -MN908947.3 23803 . TG T 116.0 PASS DP=273;AF=0.018315;SB=0;DP4=102,166,2,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2242delG|p.Glu748fs|2242/3822|2242/3822|748/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24197 . G T 92.0 PASS DP=542;AF=0.011070;SB=1;DP4=296,240,4,2;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2635G>T|p.Ala879Ser|2635/3822|2635/3822|879/1273|| -MN908947.3 24506 . T G 32597.0 PASS DP=849;AF=1.000000;SB=0;DP4=0,0,471,378;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| -MN908947.3 24672 . CA C 60.0 PASS DP=907;AF=0.004410;SB=0;DP4=396,507,2,2;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3111delA|p.Arg1039fs|3111/3822|3111/3822|1037/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24821 . G C 76.0 PASS DP=1161;AF=0.005168;SB=0;DP4=594,561,3,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3259G>C|p.Ala1087Pro|3259/3822|3259/3822|1087/1273|| -MN908947.3 24914 . G C 46451.0 PASS DP=1236;AF=1.000000;SB=0;DP4=0,0,611,625;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| -MN908947.3 24931 . TG T 66.0 PASS DP=1143;AF=0.003500;SB=0;DP4=559,580,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3370delG|p.Gly1124fs|3370/3822|3370/3822|1124/1273||;LOF=(S|gene-GU280_gp02|1|1.00) -MN908947.3 24959 . G T 80.0 PASS DP=963;AF=0.006231;SB=0;DP4=434,521,3,3;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3397G>T|p.Val1133Phe|3397/3822|3397/3822|1133/1273|| -MN908947.3 25186 . G C 74.0 PASS DP=1157;AF=0.005186;SB=0;DP4=574,577,3,3;ANN=C|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3624G>C|p.Gln1208His|3624/3822|3624/3822|1208/1273|| -MN908947.3 25301 . TG T 71.0 PASS DP=719;AF=0.005563;SB=0;DP4=304,412,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3740delG|p.Cys1247fs|3740/3822|3740/3822|1247/1273|| -MN908947.3 25314 . G T 81.0 PASS DP=707;AF=0.008487;SB=1;DP4=323,378,2,4;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3752G>T|p.Gly1251Val|3752/3822|3752/3822|1251/1273|| -MN908947.3 25317 . C G 84.0 PASS DP=697;AF=0.008608;SB=1;DP4=317,374,2,4;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3755C>G|p.Ser1252Cys|3755/3822|3755/3822|1252/1273|| -MN908947.3 25325 . A T 70.0 PASS DP=680;AF=0.007353;SB=7;DP4=307,368,4,1;ANN=T|stop_gained|HIGH|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.3763A>T|p.Lys1255*|3763/3822|3763/3822|1255/1273|| -MN908947.3 25608 . A C 71.0 PASS DP=439;AF=0.011390;SB=15;DP4=127,307,4,1;ANN=C|synonymous_variant|LOW|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.216A>C|p.Ala72Ala|216/828|216/828|72/275|| -MN908947.3 25628 . TTG T 58.0 PASS DP=466;AF=0.006438;SB=2;DP4=223,242,2,1;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.237_238delTG|p.Val80fs|237/828|237/828|79/275||;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 25629 . TG T 58.0 PASS DP=466;AF=0.006438;SB=0;DP4=223,242,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.238delG|p.Val80fs|238/828|238/828|80/275||;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 26157 . TGTTA T 68.0 PASS DP=1010;AF=0.003960;SB=0;DP4=501,510,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.766_769delGTTA|p.Val256fs|766/828|766/828|256/275||;LOF=(ORF3a|gene-GU280_gp03|1|1.00) -MN908947.3 26209 . G T 63.0 PASS DP=840;AF=0.005952;SB=0;DP4=363,472,2,3;ANN=T|missense_variant|MODERATE|ORF3a|gene-GU280_gp03|transcript|TRANSCRIPT_gene-GU280_gp03|protein_coding|1/1|c.817G>T|p.Val273Leu|817/828|817/828|273/275|| -MN908947.3 26261 . CG C 108.0 PASS DP=886;AF=0.006772;SB=3;DP4=470,410,2,4;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.18delG|p.Glu7fs|18/228|18/228|6/75||;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26354 . TTCG T 66.0 PASS DP=1142;AF=0.003503;SB=0;DP4=570,568,2,2;INDEL;HRUN=2;ANN=T|disruptive_inframe_deletion|MODERATE|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.111_113delTCG|p.Arg38del|111/228|111/228|37/75|| -MN908947.3 26366 . CG C 66.0 PASS DP=1197;AF=0.003342;SB=0;DP4=594,599,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.123delG|p.Tyr42fs|123/228|123/228|41/75||;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26367 . G T 136.0 PASS DP=1200;AF=0.008333;SB=0;DP4=590,596,5,5;ANN=T|synonymous_variant|LOW|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.123G>T|p.Ala41Ala|123/228|123/228|41/75|| -MN908947.3 26408 . CT C 59.0 PASS DP=1171;AF=0.003416;SB=0;DP4=571,596,2,2;INDEL;HRUN=5;ANN=C|frameshift_variant|HIGH|E|gene-GU280_gp04|transcript|TRANSCRIPT_gene-GU280_gp04|protein_coding|1/1|c.165delT|p.Tyr57fs|165/228|165/228|55/75||;LOF=(E|gene-GU280_gp04|1|1.00) -MN908947.3 26713 . GT G 133.0 PASS DP=1343;AF=0.005957;SB=0;DP4=691,649,4,4;INDEL;HRUN=4;ANN=G|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.192delT|p.Phe65fs|192/669|192/669|64/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26720 . G A 127.0 PASS DP=1331;AF=0.007513;SB=0;DP4=673,646,5,5;ANN=A|synonymous_variant|LOW|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.198G>A|p.Val66Val|198/669|198/669|66/222|| -MN908947.3 26721 . CTT C 170.0 PASS DP=1321;AF=0.007570;SB=0;DP4=673,648,5,5;INDEL;HRUN=2;ANN=C|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.200_201delTT|p.Leu67fs|200/669|200/669|67/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26736 . AG A 64.0 PASS DP=1315;AF=0.003042;SB=0;DP4=666,645,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.215delG|p.Arg72fs|215/669|215/669|72/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 26776 . CTTG C 65.0 PASS DP=1246;AF=0.003210;SB=0;DP4=598,651,2,2;INDEL;HRUN=2;ANN=C|conservative_inframe_deletion|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.255_257delTTG|p.Cys86del|255/669|255/669|85/222|| -MN908947.3 26783 . TG T 99.0 PASS DP=1067;AF=0.005623;SB=1;DP4=469,636,3,3;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.262delG|p.Val88fs|262/669|262/669|88/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 27029 . TG T 51.0 PASS DP=855;AF=0.003509;SB=0;DP4=418,434,1,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.508delG|p.Val170fs|508/669|508/669|170/222||;LOF=(M|gene-GU280_gp05|1|1.00) -MN908947.3 27052 . CTTA C 72.0 PASS DP=857;AF=0.004667;SB=0;DP4=414,439,2,2;INDEL;HRUN=2;ANN=C|conservative_inframe_deletion|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.531_533delTTA|p.Tyr178del|531/669|531/669|177/222|| -MN908947.3 27183 . G C 167.0 PASS DP=861;AF=0.012776;SB=2;DP4=512,337,8,3;ANN=C|missense_variant|MODERATE|M|gene-GU280_gp05|transcript|TRANSCRIPT_gene-GU280_gp05|protein_coding|1/1|c.661G>C|p.Val221Leu|661/669|661/669|221/222|| -MN908947.3 27194 . GACAACAGATGTTTCATCTCGTTGACTT G 69.0 PASS DP=951;AF=0.004206;SB=1;DP4=607,365,2,2;INDEL;HRUN=1;ANN=G|frameshift_variant&start_lost|HIGH|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.-7_20delACAACAGATGTTTCATCTCGTTGACTT|p.Met1fs||1/186|1/61||;LOF=(ORF6|gene-GU280_gp06|1|1.00) -MN908947.3 27281 . G C 67.0 PASS DP=1702;AF=0.003525;SB=0;DP4=847,839,3,3;ANN=C|missense_variant|MODERATE|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.80G>C|p.Trp27Ser|80/186|80/186|27/61|| -MN908947.3 27366 . G T 94.0 PASS DP=1764;AF=0.004535;SB=0;DP4=869,885,4,4;ANN=T|missense_variant|MODERATE|ORF6|gene-GU280_gp06|transcript|TRANSCRIPT_gene-GU280_gp06|protein_coding|1/1|c.165G>T|p.Glu55Asp|165/186|165/186|55/61|| -MN908947.3 27394 . ATG A 78.0 PASS DP=1653;AF=0.003025;SB=1;DP4=804,845,3,2;INDEL;HRUN=1;ANN=A|frameshift_variant&start_lost|HIGH|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.2_3delTG|p.Met1fs|2/366|2/366|1/121||;LOF=(ORF7a|gene-GU280_gp07|1|1.00) -MN908947.3 27476 . C T 102.0 PASS DP=683;AF=0.013177;SB=0;DP4=232,442,3,6;ANN=T|missense_variant|MODERATE|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.83C>T|p.Thr28Ile|83/366|83/366|28/121|| -MN908947.3 27494 . C T 137.0 PASS DP=495;AF=0.018182;SB=1;DP4=158,328,2,7;ANN=T|missense_variant|MODERATE|ORF7a|gene-GU280_gp07|transcript|TRANSCRIPT_gene-GU280_gp07|protein_coding|1/1|c.101C>T|p.Pro34Leu|101/366|101/366|34/121|| -MN908947.3 27972 . C T 18460.0 PASS DP=481;AF=1.000000;SB=0;DP4=0,0,245,236;ANN=T|stop_gained|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| -MN908947.3 28000 . CG C 81.0 PASS DP=482;AF=0.008299;SB=0;DP4=242,236,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.108delG|p.Cys37fs|108/366|108/366|36/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28048 . G T 15365.0 PASS DP=404;AF=0.995049;SB=0;DP4=0,0,196,208;ANN=T|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| -MN908947.3 28073 . G C 64.0 PASS DP=322;AF=0.012422;SB=0;DP4=131,187,2,2;ANN=C|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.180G>C|p.Leu60Phe|180/366|180/366|60/121|| -MN908947.3 28111 . A G 18931.0 PASS DP=519;AF=0.996146;SB=0;DP4=0,0,321,198;ANN=G|missense_variant|MODERATE|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| -MN908947.3 28196 . TTG T 50.0 PASS DP=936;AF=0.003205;SB=0;DP4=527,406,2,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.304_305delTG|p.Cys102fs|304/366|304/366|102/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28197 . TG T 69.0 PASS DP=950;AF=0.004211;SB=0;DP4=530,416,2,2;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.305delG|p.Cys102fs|305/366|305/366|102/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28207 . ATG A 68.0 PASS DP=1036;AF=0.003861;SB=0;DP4=542,490,2,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.315_316delTG|p.Tyr105fs|315/366|315/366|105/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28214 . C CT 60.0 PASS DP=1052;AF=0.003802;SB=0;DP4=546,505,2,2;INDEL;HRUN=5;ANN=CT|frameshift_variant|HIGH|ORF8|gene-GU280_gp09|transcript|TRANSCRIPT_gene-GU280_gp09|protein_coding|1/1|c.321_322insT|p.Leu109fs|322/366|322/366|108/121||;LOF=(ORF8|gene-GU280_gp09|1|1.00) -MN908947.3 28270 . TA T 22586.0 PASS DP=1102;AF=0.956443;SB=0;DP4=26,24,532,522;INDEL;HRUN=4 -MN908947.3 28280 . G C 22789.0 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520;ANN=C|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.7G>C|p.Asp3His|7/1260|7/1260|3/419|| -MN908947.3 28281 . A T 22802.0 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520;ANN=T|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.8A>T|p.Asp3Val|8/1260|8/1260|3/419|| -MN908947.3 28282 . T A 22760.0 PASS DP=1052;AF=0.997148;SB=0;DP4=1,1,530,520;ANN=A|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.9T>A|p.Asp3Glu|9/1260|9/1260|3/419|| -MN908947.3 28324 . TG T 67.0 PASS DP=1086;AF=0.003683;SB=0;DP4=535,548,2,2;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.52delG|p.Gly18fs|52/1260|52/1260|18/419|| -MN908947.3 28406 . T TA 168.0 PASS DP=590;AF=0.013559;SB=1;DP4=198,388,2,6;INDEL;HRUN=3;ANN=TA|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.133_134insA|p.Leu45fs|134/1260|134/1260|45/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 28881 . G A 21462.0 PASS DP=563;AF=0.996448;SB=0;DP4=1,1,290,271;ANN=A|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.608G>A|p.Arg203Lys|608/1260|608/1260|203/419|| -MN908947.3 28882 . G A 20841.0 PASS DP=561;AF=0.991087;SB=0;DP4=1,1,288,271;ANN=A|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.609G>A|p.Arg203Arg|609/1260|609/1260|203/419|| -MN908947.3 28883 . G C 21251.0 PASS DP=562;AF=0.994662;SB=0;DP4=1,1,287,272;ANN=C|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.610G>C|p.Gly204Arg|610/1260|610/1260|204/419|| -MN908947.3 28886 . A G 83.0 PASS DP=564;AF=0.010638;SB=0;DP4=286,272,3,3;ANN=G|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.613A>G|p.Thr205Ala|613/1260|613/1260|205/419|| -MN908947.3 28977 . C T 9754.0 PASS DP=254;AF=1.000000;SB=0;DP4=0,0,26,228;ANN=T|missense_variant|MODERATE|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| -MN908947.3 29104 . TG T 76.0 PASS DP=634;AF=0.006309;SB=1;DP4=356,274,3,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.832delG|p.Gly278fs|832/1260|832/1260|278/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29144 . C T 731.0 PASS DP=763;AF=0.045872;SB=3;DP4=382,346,16,19;ANN=T|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.871C>T|p.Leu291Leu|871/1260|871/1260|291/419|| -MN908947.3 29178 . CG C 74.0 PASS DP=753;AF=0.005312;SB=0;DP4=391,358,2,2;INDEL;HRUN=1;ANN=C|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.906delG|p.Gln303fs|906/1260|906/1260|302/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29281 . C T 116.0 PASS DP=475;AF=0.014737;SB=1;DP4=198,270,2,5;ANN=T|synonymous_variant|LOW|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.1008C>T|p.Ala336Ala|1008/1260|1008/1260|336/419|| -MN908947.3 29353 . C CA 52.0 PASS DP=605;AF=0.004959;SB=0;DP4=338,279,2,1;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|N|gene-GU280_gp10|transcript|TRANSCRIPT_gene-GU280_gp10|protein_coding|1/1|c.1080_1081insA|p.Thr362fs|1081/1260|1081/1260|361/419||;LOF=(N|gene-GU280_gp10|1|1.00) -MN908947.3 29543 . G T 65.0 PASS DP=1553;AF=0.005151;SB=0;DP4=814,729,4,4 -MN908947.3 29642 . C T 169.0 PASS DP=1375;AF=0.008727;SB=6;DP4=605,756,3,9;ANN=T|stop_gained|HIGH|ORF10|gene-GU280_gp11|transcript|TRANSCRIPT_gene-GU280_gp11|protein_coding|1/1|c.85C>T|p.Gln29*|85/117|85/117|29/38|| -MN908947.3 29645 . G T 101.0 PASS DP=1352;AF=0.005917;SB=0;DP4=600,742,4,4;ANN=T|missense_variant|MODERATE|ORF10|gene-GU280_gp11|transcript|TRANSCRIPT_gene-GU280_gp11|protein_coding|1/1|c.88G>T|p.Val30Leu|88/117|88/117|30/38|| -MN908947.3 29736 . G T 80.0 PASS DP=868;AF=0.006912;SB=0;DP4=419,443,3,3 -MN908947.3 29748 . TACG T 51.0 PASS DP=842;AF=0.003563;SB=2;DP4=401,441,2,1;INDEL;HRUN=1 diff --git a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter01.vcf b/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter01.vcf deleted file mode 100644 index 5f62e8c..0000000 --- a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter01.vcf +++ /dev/null @@ -1,53 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5229917/ERR5229917.preprocessed.lofreq.vcf ERR5229917/ERR5229917.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.1' ./ERR5229917/ERR5229917.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:45 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 29888 PASS DP=800;AF=0.995;SB=0;DP4=1,1,390,406 -MN908947.3 913 . C T 35817 PASS DP=931;AF=1;SB=0;DP4=0,0,417,514 -MN908947.3 3037 . C T 31757 PASS DP=825;AF=1;SB=0;DP4=0,0,371,454 -MN908947.3 3177 . C T 19987 PASS DP=545;AF=0.990826;SB=0;DP4=1,1,304,239 -MN908947.3 3267 . C T 43568 PASS DP=1150;AF=0.998261;SB=0;DP4=0,0,590,560 -MN908947.3 5388 . C A 42501 PASS DP=1107;AF=1;SB=0;DP4=0,0,559,548 -MN908947.3 5986 . C T 21855 PASS DP=582;AF=1;SB=0;DP4=0,0,327,255 -MN908947.3 6954 . T C 28841 PASS DP=750;AF=0.998667;SB=0;DP4=0,0,358,392 -MN908947.3 11287 . GTCTGGTTTT G 45483 PASS DP=1355;AF=0.99631;SB=71;DP4=69,33,541,809;INDEL;HRUN=1 -MN908947.3 14408 . C T 42523 PASS DP=1109;AF=0.996393;SB=0;DP4=0,0,553,553 -MN908947.3 14676 . C T 49314 PASS DP=1416;AF=0.995763;SB=0;DP4=3,3,718,692 -MN908947.3 15279 . C T 41710 PASS DP=1117;AF=0.998209;SB=0;DP4=0,0,615,502 -MN908947.3 16176 . T C 32264 PASS DP=875;AF=0.998857;SB=0;DP4=0,0,446,429 -MN908947.3 21764 . ATACATG A 16780 PASS DP=449;AF=0.986637;SB=0;DP4=2,2,244,199;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 8304 PASS DP=243;AF=0.876543;SB=7;DP4=12,21,107,106;INDEL;HRUN=3 -MN908947.3 23063 . A T 10180 PASS DP=264;AF=0.996212;SB=0;DP4=0,0,132,132 -MN908947.3 23271 . C A 44093 PASS DP=1158;AF=0.996546;SB=0;DP4=1,1,591,563 -MN908947.3 23403 . A G 42730 PASS DP=1137;AF=0.995602;SB=0;DP4=0,0,496,637 -MN908947.3 23604 . C A 37398 PASS DP=988;AF=0.995951;SB=0;DP4=0,0,485,503 -MN908947.3 23709 . C T 21391 PASS DP=553;AF=1;SB=0;DP4=0,0,96,457 -MN908947.3 24506 . T G 32597 PASS DP=849;AF=1;SB=0;DP4=0,0,471,378 -MN908947.3 24914 . G C 46451 PASS DP=1236;AF=1;SB=0;DP4=0,0,611,625 -MN908947.3 27972 . C T 18460 PASS DP=481;AF=1;SB=0;DP4=0,0,245,236 -MN908947.3 28048 . G T 15365 PASS DP=404;AF=0.995049;SB=0;DP4=0,0,196,208 -MN908947.3 28111 . A G 18931 PASS DP=519;AF=0.996146;SB=0;DP4=0,0,321,198 -MN908947.3 28270 . TA T 22586 PASS DP=1102;AF=0.956443;SB=0;DP4=26,24,532,522;INDEL;HRUN=4 -MN908947.3 28280 . G C 22789 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520 -MN908947.3 28281 . A T 22802 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520 -MN908947.3 28282 . T A 22760 PASS DP=1052;AF=0.997148;SB=0;DP4=1,1,530,520 -MN908947.3 28881 . G A 21462 PASS DP=563;AF=0.996448;SB=0;DP4=1,1,290,271 -MN908947.3 28882 . G A 20841 PASS DP=561;AF=0.991087;SB=0;DP4=1,1,288,271 -MN908947.3 28883 . G C 21251 PASS DP=562;AF=0.994662;SB=0;DP4=1,1,287,272 -MN908947.3 28977 . C T 9754 PASS DP=254;AF=1;SB=0;DP4=0,0,26,228 diff --git a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter02.vcf b/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter02.vcf deleted file mode 100644 index ce08871..0000000 --- a/benchmark/ERR5229917/ERR5229917.preprocessed.lofreq.vcf.filter02.vcf +++ /dev/null @@ -1,53 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5229917/ERR5229917.preprocessed.lofreq.vcf ERR5229917/ERR5229917.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' ./ERR5229917/ERR5229917.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:45 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 29888 PASS DP=800;AF=0.995;SB=0;DP4=1,1,390,406 -MN908947.3 913 . C T 35817 PASS DP=931;AF=1;SB=0;DP4=0,0,417,514 -MN908947.3 3037 . C T 31757 PASS DP=825;AF=1;SB=0;DP4=0,0,371,454 -MN908947.3 3177 . C T 19987 PASS DP=545;AF=0.990826;SB=0;DP4=1,1,304,239 -MN908947.3 3267 . C T 43568 PASS DP=1150;AF=0.998261;SB=0;DP4=0,0,590,560 -MN908947.3 5388 . C A 42501 PASS DP=1107;AF=1;SB=0;DP4=0,0,559,548 -MN908947.3 5986 . C T 21855 PASS DP=582;AF=1;SB=0;DP4=0,0,327,255 -MN908947.3 6954 . T C 28841 PASS DP=750;AF=0.998667;SB=0;DP4=0,0,358,392 -MN908947.3 11287 . GTCTGGTTTT G 45483 PASS DP=1355;AF=0.99631;SB=71;DP4=69,33,541,809;INDEL;HRUN=1 -MN908947.3 14408 . C T 42523 PASS DP=1109;AF=0.996393;SB=0;DP4=0,0,553,553 -MN908947.3 14676 . C T 49314 PASS DP=1416;AF=0.995763;SB=0;DP4=3,3,718,692 -MN908947.3 15279 . C T 41710 PASS DP=1117;AF=0.998209;SB=0;DP4=0,0,615,502 -MN908947.3 16176 . T C 32264 PASS DP=875;AF=0.998857;SB=0;DP4=0,0,446,429 -MN908947.3 21764 . ATACATG A 16780 PASS DP=449;AF=0.986637;SB=0;DP4=2,2,244,199;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 8304 PASS DP=243;AF=0.876543;SB=7;DP4=12,21,107,106;INDEL;HRUN=3 -MN908947.3 23063 . A T 10180 PASS DP=264;AF=0.996212;SB=0;DP4=0,0,132,132 -MN908947.3 23271 . C A 44093 PASS DP=1158;AF=0.996546;SB=0;DP4=1,1,591,563 -MN908947.3 23403 . A G 42730 PASS DP=1137;AF=0.995602;SB=0;DP4=0,0,496,637 -MN908947.3 23604 . C A 37398 PASS DP=988;AF=0.995951;SB=0;DP4=0,0,485,503 -MN908947.3 23709 . C T 21391 PASS DP=553;AF=1;SB=0;DP4=0,0,96,457 -MN908947.3 24506 . T G 32597 PASS DP=849;AF=1;SB=0;DP4=0,0,471,378 -MN908947.3 24914 . G C 46451 PASS DP=1236;AF=1;SB=0;DP4=0,0,611,625 -MN908947.3 27972 . C T 18460 PASS DP=481;AF=1;SB=0;DP4=0,0,245,236 -MN908947.3 28048 . G T 15365 PASS DP=404;AF=0.995049;SB=0;DP4=0,0,196,208 -MN908947.3 28111 . A G 18931 PASS DP=519;AF=0.996146;SB=0;DP4=0,0,321,198 -MN908947.3 28270 . TA T 22586 PASS DP=1102;AF=0.956443;SB=0;DP4=26,24,532,522;INDEL;HRUN=4 -MN908947.3 28280 . G C 22789 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520 -MN908947.3 28281 . A T 22802 PASS DP=1052;AF=0.998099;SB=0;DP4=1,1,530,520 -MN908947.3 28282 . T A 22760 PASS DP=1052;AF=0.997148;SB=0;DP4=1,1,530,520 -MN908947.3 28881 . G A 21462 PASS DP=563;AF=0.996448;SB=0;DP4=1,1,290,271 -MN908947.3 28882 . G A 20841 PASS DP=561;AF=0.991087;SB=0;DP4=1,1,288,271 -MN908947.3 28883 . G C 21251 PASS DP=562;AF=0.994662;SB=0;DP4=1,1,287,272 -MN908947.3 28977 . C T 9754 PASS DP=254;AF=1;SB=0;DP4=0,0,26,228 diff --git a/benchmark/ERR5229917/ERR5229917.vcf b/benchmark/ERR5229917/ERR5229917.vcf deleted file mode 100644 index 4cfa4e1..0000000 --- a/benchmark/ERR5229917/ERR5229917.vcf +++ /dev/null @@ -1,63 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5229917.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5229917.vcf; Date=Mon Jun 7 15:46:05 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=131;VDB=1.4224e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,78,48;MQ=60 GT:PL:AD 1:255,0:0,126 -MN908947.3 913 . C T 225.417 . DP=129;VDB=6.20234e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,52;MQ=60 GT:PL:AD 1:255,0:0,127 -MN908947.3 3037 . C T 225.417 . DP=111;VDB=4.91991e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,53;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 3177 . C T 228.395 . DP=72;VDB=1;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,41,28;MQ=60 GT:PL:AD 1:255,0:1,69 -MN908947.3 3267 . C T 225.417 . DP=113;VDB=0.000108359;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,70,38;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 5388 . C A 225.417 . DP=109;VDB=0.000332757;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,41;MQ=60 GT:PL:AD 1:255,0:0,107 -MN908947.3 5986 . C T 225.417 . DP=77;VDB=1.57378e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,45,28;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 6954 . T C 225.417 . DP=111;VDB=1.06073e-08;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,53;MQ=60 GT:PL:AD 1:255,0:0,109 -MN908947.3 11287 . GTCTGGTTTT G 228.393 . INDEL;IDV=132;IMF=0.94964;DP=139;VDB=1.88453e-08;SGB=-0.693147;MQSB=0.979246;MQ0F=0;AC=1;AN=1;DP4=5,2,87,45;MQ=59 GT:PL:AD 1:255,0:7,132 -MN908947.3 11296 . T G 14.5687 . DP=3;VDB=0.14;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,2,0;MQ=60 GT:PL:AD 1:44,0:0,2 -MN908947.3 14408 . C T 225.417 . DP=125;VDB=1.43995e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,46;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 14676 . C T 228.409 . DP=121;VDB=1.56534e-06;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,83,34;MQ=60 GT:PL:AD 1:255,0:1,117 -MN908947.3 15279 . C T 225.417 . DP=98;VDB=0.00245807;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,69,27;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 16176 . T C 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,21;MQ=60 GT:PL:AD 1:255,0:0,80 -MN908947.3 21764 . ATACATGTCT ATCT 225.421 . INDEL;IDV=60;IMF=1;DP=60;VDB=1.55058e-07;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,22;MQ=60 GT:PL:AD 1:255,0:0,59 -MN908947.3 21990 . TTTATTA TTTA 178.235 . INDEL;IDV=43;IMF=0.843137;DP=51;VDB=0.999998;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=6,3,27,15;MQ=60 GT:PL:AD 1:255,50:9,42 -MN908947.3 23063 . A T 225.417 . DP=90;VDB=0.111568;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,28;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 23271 . C A 228.41 . DP=126;VDB=0.000148154;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,81,39;MQ=60 GT:PL:AD 1:255,0:1,120 -MN908947.3 23403 . A G 225.417 . DP=142;VDB=8.79877e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,91,47;MQ=60 GT:PL:AD 1:255,0:0,138 -MN908947.3 23604 . C A 225.417 . DP=109;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,44;MQ=60 GT:PL:AD 1:255,0:0,104 -MN908947.3 23709 . C T 225.417 . DP=79;VDB=8.52388e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,30,48;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 24506 . T G 225.417 . DP=103;VDB=0.0210185;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,33;MQ=60 GT:PL:AD 1:255,0:0,97 -MN908947.3 24914 . G C 225.417 . DP=141;VDB=0.00368073;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,48;MQ=60 GT:PL:AD 1:255,0:0,134 -MN908947.3 27972 . C T 225.417 . DP=95;VDB=0.00177412;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,51,40;MQ=60 GT:PL:AD 1:255,0:0,91 -MN908947.3 28048 . G T 225.417 . DP=94;VDB=0.00104892;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,46;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 28111 . A G 225.417 . DP=81;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,32;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 28270 . TAAAA TAAA 59.0943 . INDEL;IDV=121;IMF=0.937984;DP=129;VDB=0.000210326;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=9,8,73,39;MQ=60 GT:PL:AD 1:86,0:17,112 -MN908947.3 28274 . A T 9.88514 . DP=122;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:39,0:0,1 -MN908947.3 28280 . G C 225.417 . DP=120;VDB=8.64822e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28281 . A T 225.417 . DP=120;VDB=8.10825e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28282 . T A 225.417 . DP=120;VDB=6.34296e-10;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,44;MQ=60 GT:PL:AD 1:255,0:0,119 -MN908947.3 28881 . G A 225.417 . DP=108;VDB=3.77072e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,46;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28882 . G A 225.417 . DP=107;VDB=1.39355e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28883 . G C 225.417 . DP=108;VDB=1.29056e-06;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,47;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 28977 . C T 225.417 . DP=69;VDB=0.305786;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,14,55;MQ=60 GT:PL:AD 1:255,0:0,69 diff --git a/benchmark/ERR5397623/ERR5397623.annotated.vcf b/benchmark/ERR5397623/ERR5397623.annotated.vcf deleted file mode 100644 index e6b8206..0000000 --- a/benchmark/ERR5397623/ERR5397623.annotated.vcf +++ /dev/null @@ -1,75 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5397623/ERR5397623.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5397623.vcf; Date=Mon Jun 7 15:52:25 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:52:39 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5397623.normalized.vcf -; Date=Mon Jun 7 15:52:39 2021 -##bcftools/csqVersion=1.12+htslib-1.12 -##bcftools/csqCommand=csq --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --gff-annot /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.101.gff3 -o ERR5397623.annotated.vcf /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5397623/ERR5397623.normalized.vcf; Date=Mon Jun 7 15:52:40 2021 -##INFO= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=107;VDB=0.631715;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,32;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 277 . T C 225.417 . DP=105;VDB=0.301872;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,42;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|4L|277T>C,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4L|277T>C GT:PL:AD:BCSQ 1:255,0:0,101:5 -MN908947.3 913 . C T 225.417 . DP=95;VDB=0.0116183;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,29;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|216S|913C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|216S|913C>T GT:PL:AD:BCSQ 1:255,0:0,90:5 -MN908947.3 2453 . C T 225.417 . DP=99;VDB=0.726511;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,48,48;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|730L>730F|2453C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|730L>730F|2453C>T GT:PL:AD:BCSQ 1:255,0:0,96:5 -MN908947.3 3037 . C T 225.422 . DP=112;VDB=0.047627;SGB=-0.693147;MQSB=0.979803;MQ0F=0;AC=1;AN=1;DP4=0,0,62,43;MQ=59;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|924F|3037C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|924F|3037C>T GT:PL:AD:BCSQ 1:255,0:0,104:5 -MN908947.3 3267 . C T 225.417 . DP=104;VDB=0.728207;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,18;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1001T>1001I|3267C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1001T>1001I|3267C>T GT:PL:AD:BCSQ 1:255,0:0,100:5 -MN908947.3 4891 . C T 228.405 . DP=104;VDB=0.413458;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,49;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1542T|4891C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1542T|4891C>T GT:PL:AD:BCSQ 1:255,0:1,96:5 -MN908947.3 5388 . C A 225.417 . DP=96;VDB=0.132707;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,19;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1708A>1708D|5388C>A,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1708A>1708D|5388C>A GT:PL:AD:BCSQ 1:255,0:0,86:5 -MN908947.3 5986 . C T 225.417 . DP=83;VDB=0.0647342;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,16;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1907F|5986C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1907F|5986C>T GT:PL:AD:BCSQ 1:255,0:0,79:5 -MN908947.3 6322 . T A 225.417 . DP=102;VDB=0.367309;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,71,27;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|2019V|6322T>A,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|2019V|6322T>A GT:PL:AD:BCSQ 1:255,0:0,98:5 -MN908947.3 6954 . T C 225.417 . DP=90;VDB=0.201374;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,44;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2230I>2230T|6954T>C,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2230I>2230T|6954T>C GT:PL:AD:BCSQ 1:255,0:0,84:5 -MN908947.3 9163 . C T 225.417 . DP=106;VDB=0.102543;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,34;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|2966N|9163C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|2966N|9163C>T GT:PL:AD:BCSQ 1:255,0:0,90:5 -MN908947.3 11287 . GTCTGGTTTT G 228.408 . INDEL;IDV=104;IMF=0.962963;DP=108;VDB=0.000667777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,71,30;MQ=60;BCSQ=inframe_deletion|ORF1ab|ENSSAST00005000003|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G,inframe_deletion|ORF1ab|ENSSAST00005000002|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G GT:PL:AD:BCSQ 1:255,0:7,101:5 -MN908947.3 14408 . C T 225.417 . DP=106;VDB=0.249649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,32;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4715L|14408C>T GT:PL:AD:BCSQ 1:255,0:0,99:1 -MN908947.3 14676 . C T 225.417 . DP=121;VDB=0.107184;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|4804P>4801L|14676C>T GT:PL:AD:BCSQ 1:255,0:0,118:1 -MN908947.3 15279 . C T 225.417 . DP=83;VDB=0.0200448;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,15;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5005T>5002I|15279C>T GT:PL:AD:BCSQ 1:255,0:0,75:1 -MN908947.3 16176 . T C 225.417 . DP=72;VDB=0.999978;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,17;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5304L>5301P|16176T>C GT:PL:AD:BCSQ 1:255,0:0,63:1 -MN908947.3 21764 . ATACATG A 228.36 . INDEL;IDV=71;IMF=0.946667;DP=75;VDB=0.00709019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,2,51,20;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|68IHV>68I|21764ATACATG>A GT:PL:AD:BCSQ 1:255,0:4,71:1 -MN908947.3 21990 . TTTA T 141.204 . INDEL;IDV=48;IMF=0.8;DP=60;VDB=0.999506;SGB=-0.693147;MQSB=0.986846;MQ0F=0;AC=1;AN=1;DP4=5,8,34,13;MQ=59;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|143VY>141V|21990TTTA>T GT:PL:AD:BCSQ 1:255,87:13,47:1 -MN908947.3 21991 . TTA T 97.7941 . INDEL;IDV=1;IMF=0.0175439;DP=57;VDB=0.999337;SGB=-0.69311;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=17,9,20,11;MQ=60;OLD_CLUMPED=MN908947.3|21991|TTAT|TT GT:PL:AD 1:183,58:26,31 -MN908947.3 23063 . A T 225.417 . DP=19;VDB=0.970247;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,6,12;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|501N>498Y|23063A>T GT:PL:AD:BCSQ 1:255,0:0,18:1 -MN908947.3 23271 . C A 225.417 . DP=120;VDB=0.849019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,27;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|570A>567D|23271C>A GT:PL:AD:BCSQ 1:255,0:0,117:1 -MN908947.3 23403 . A G 225.417 . DP=116;VDB=0.255022;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,30;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|614D>611G|23403A>G GT:PL:AD:BCSQ 1:255,0:0,106:1 -MN908947.3 23604 . C A 225.417 . DP=102;VDB=0.122654;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,24;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|681P>678H|23604C>A GT:PL:AD:BCSQ 1:255,0:0,96:1 -MN908947.3 23709 . C T 225.417 . DP=105;VDB=0.00948335;SGB=-0.693147;MQSB=0.990148;MQ0F=0.00952381;AC=1;AN=1;DP4=0,0,60,40;MQ=59;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|716T>713I|23709C>T GT:PL:AD:BCSQ 1:255,0:0,100:1 -MN908947.3 24506 . T G 225.417 . DP=77;VDB=0.00632777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,14;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|982S>979A|24506T>G GT:PL:AD:BCSQ 1:255,0:0,74:1 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.827713;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,65,45;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|1118D>1115H|24914G>C GT:PL:AD:BCSQ 1:255,0:0,110:1 -MN908947.3 27972 . C T 225.417 . DP=104;VDB=0.903335;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,38;MQ=60;BCSQ=stop_gained|ORF8|ENSSAST00005000008|protein_coding|+|27Q>27*|27972C>T GT:PL:AD:BCSQ 1:255,0:0,98:1 -MN908947.3 28048 . G T 225.417 . DP=97;VDB=0.339895;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,43;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|52R>52I|28048G>T GT:PL:AD:BCSQ 1:255,0:0,89:1 -MN908947.3 28111 . A G 225.417 . DP=78;VDB=0.815;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,23;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|73Y>73C|28111A>G GT:PL:AD:BCSQ 1:255,0:0,70:1 -MN908947.3 28270 . TA T 9.28705 . INDEL;IDV=91;IMF=0.858491;DP=106;VDB=0.741118;SGB=-0.693147;MQSB=0.993956;MQ0F=0;AC=1;AN=1;DP4=19,10,55,22;MQ=59;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:113,77:29,77 -MN908947.3 28280 . G C 225.417 . DP=91;VDB=0.0245211;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|3D>3L|28280G>C+28281A>T+28282T>A GT:PL:AD:BCSQ 1:255,0:0,88:1 -MN908947.3 28281 . A T 228.367 . DP=91;VDB=0.0109476;SGB=-0.693147;RPB=0.836342;MQB=0.620315;MQSB=0.992166;BQB=0.299824;MQ0F=0;AC=1;AN=1;DP4=2,1,58,27;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:3,85:1 -MN908947.3 28282 . T A 225.417 . DP=92;VDB=0.0227728;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,88:1 -MN908947.3 28881 . G A 225.422 . DP=98;VDB=0.0635294;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|203R>203K|28881G>A+28882G>A GT:PL:AD:BCSQ 1:255,0:0,94:1 -MN908947.3 28882 . G A 225.417 . DP=98;VDB=0.0651209;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60;BCSQ=@28881 GT:PL:AD:BCSQ 1:255,0:0,95:1 -MN908947.3 28883 . G C 225.417 . DP=99;VDB=0.0583443;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|204G>204R|28883G>C GT:PL:AD:BCSQ 1:255,0:0,95:1 -MN908947.3 28977 . C T 225.417 . DP=63;VDB=0.004806;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,29;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|235S>235F|28977C>T GT:PL:AD:BCSQ 1:255,0:0,60:1 diff --git a/benchmark/ERR5397623/ERR5397623.normalized.vcf b/benchmark/ERR5397623/ERR5397623.normalized.vcf deleted file mode 100644 index a5077e4..0000000 --- a/benchmark/ERR5397623/ERR5397623.normalized.vcf +++ /dev/null @@ -1,71 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5397623/ERR5397623.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5397623.vcf; Date=Mon Jun 7 15:52:25 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:52:39 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5397623.normalized.vcf -; Date=Mon Jun 7 15:52:39 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=107;VDB=0.631715;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,32;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 277 . T C 225.417 . DP=105;VDB=0.301872;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,42;MQ=60 GT:PL:AD 1:255,0:0,101 -MN908947.3 913 . C T 225.417 . DP=95;VDB=0.0116183;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,29;MQ=60 GT:PL:AD 1:255,0:0,90 -MN908947.3 2453 . C T 225.417 . DP=99;VDB=0.726511;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,48,48;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 3037 . C T 225.422 . DP=112;VDB=0.047627;SGB=-0.693147;MQSB=0.979803;MQ0F=0;AC=1;AN=1;DP4=0,0,62,43;MQ=59 GT:PL:AD 1:255,0:0,104 -MN908947.3 3267 . C T 225.417 . DP=104;VDB=0.728207;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,18;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 4891 . C T 228.405 . DP=104;VDB=0.413458;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,49;MQ=60 GT:PL:AD 1:255,0:1,96 -MN908947.3 5388 . C A 225.417 . DP=96;VDB=0.132707;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,19;MQ=60 GT:PL:AD 1:255,0:0,86 -MN908947.3 5986 . C T 225.417 . DP=83;VDB=0.0647342;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,16;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 6322 . T A 225.417 . DP=102;VDB=0.367309;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,71,27;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 6954 . T C 225.417 . DP=90;VDB=0.201374;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,44;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 9163 . C T 225.417 . DP=106;VDB=0.102543;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,34;MQ=60 GT:PL:AD 1:255,0:0,90 -MN908947.3 11287 . GTCTGGTTTT G 228.408 . INDEL;IDV=104;IMF=0.962963;DP=108;VDB=0.000667777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,71,30;MQ=60 GT:PL:AD 1:255,0:7,101 -MN908947.3 14408 . C T 225.417 . DP=106;VDB=0.249649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,32;MQ=60 GT:PL:AD 1:255,0:0,99 -MN908947.3 14676 . C T 225.417 . DP=121;VDB=0.107184;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 15279 . C T 225.417 . DP=83;VDB=0.0200448;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,15;MQ=60 GT:PL:AD 1:255,0:0,75 -MN908947.3 16176 . T C 225.417 . DP=72;VDB=0.999978;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,17;MQ=60 GT:PL:AD 1:255,0:0,63 -MN908947.3 21764 . ATACATG A 228.36 . INDEL;IDV=71;IMF=0.946667;DP=75;VDB=0.00709019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,2,51,20;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT GT:PL:AD 1:255,0:4,71 -MN908947.3 21990 . TTTA T 141.204 . INDEL;IDV=48;IMF=0.8;DP=60;VDB=0.999506;SGB=-0.693147;MQSB=0.986846;MQ0F=0;AC=1;AN=1;DP4=5,8,34,13;MQ=59;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA GT:PL:AD 1:255,87:13,47 -MN908947.3 21991 . TTA T 97.7941 . INDEL;IDV=1;IMF=0.0175439;DP=57;VDB=0.999337;SGB=-0.69311;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=17,9,20,11;MQ=60;OLD_CLUMPED=MN908947.3|21991|TTAT|TT GT:PL:AD 1:183,58:26,31 -MN908947.3 23063 . A T 225.417 . DP=19;VDB=0.970247;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,6,12;MQ=60 GT:PL:AD 1:255,0:0,18 -MN908947.3 23271 . C A 225.417 . DP=120;VDB=0.849019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,27;MQ=60 GT:PL:AD 1:255,0:0,117 -MN908947.3 23403 . A G 225.417 . DP=116;VDB=0.255022;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,30;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 23604 . C A 225.417 . DP=102;VDB=0.122654;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,24;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 23709 . C T 225.417 . DP=105;VDB=0.00948335;SGB=-0.693147;MQSB=0.990148;MQ0F=0.00952381;AC=1;AN=1;DP4=0,0,60,40;MQ=59 GT:PL:AD 1:255,0:0,100 -MN908947.3 24506 . T G 225.417 . DP=77;VDB=0.00632777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,14;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.827713;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,65,45;MQ=60 GT:PL:AD 1:255,0:0,110 -MN908947.3 27972 . C T 225.417 . DP=104;VDB=0.903335;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,38;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 28048 . G T 225.417 . DP=97;VDB=0.339895;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,43;MQ=60 GT:PL:AD 1:255,0:0,89 -MN908947.3 28111 . A G 225.417 . DP=78;VDB=0.815;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,23;MQ=60 GT:PL:AD 1:255,0:0,70 -MN908947.3 28270 . TA T 9.28705 . INDEL;IDV=91;IMF=0.858491;DP=106;VDB=0.741118;SGB=-0.693147;MQSB=0.993956;MQ0F=0;AC=1;AN=1;DP4=19,10,55,22;MQ=59;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:113,77:29,77 -MN908947.3 28280 . G C 225.417 . DP=91;VDB=0.0245211;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59 GT:PL:AD 1:255,0:0,88 -MN908947.3 28281 . A T 228.367 . DP=91;VDB=0.0109476;SGB=-0.693147;RPB=0.836342;MQB=0.620315;MQSB=0.992166;BQB=0.299824;MQ0F=0;AC=1;AN=1;DP4=2,1,58,27;MQ=59 GT:PL:AD 1:255,0:3,85 -MN908947.3 28282 . T A 225.417 . DP=92;VDB=0.0227728;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59 GT:PL:AD 1:255,0:0,88 -MN908947.3 28881 . G A 225.422 . DP=98;VDB=0.0635294;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,94 -MN908947.3 28882 . G A 225.417 . DP=98;VDB=0.0651209;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,95 -MN908947.3 28883 . G C 225.417 . DP=99;VDB=0.0583443;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,95 -MN908947.3 28977 . C T 225.417 . DP=63;VDB=0.004806;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,29;MQ=60 GT:PL:AD 1:255,0:0,60 diff --git a/benchmark/ERR5397623/ERR5397623.preprocessed.gatk.vcf b/benchmark/ERR5397623/ERR5397623.preprocessed.gatk.vcf deleted file mode 100644 index 3cd1a0e..0000000 --- a/benchmark/ERR5397623/ERR5397623.preprocessed.gatk.vcf +++ /dev/null @@ -1,64 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 23636.04 . AC=1;AF=1.00;AN=1;DP=775;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.26;SOR=0.753 GT:AD:DP:GQ:PL 1:0,756:756:99:23646,0 -MN908947.3 277 . T C 22278.04 . AC=1;AF=1.00;AN=1;DP=654;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.43;SOR=1.442 GT:AD:DP:GQ:PL 1:0,647:647:99:22288,0 -MN908947.3 913 . C T 40271.04 . AC=1;AF=1.00;AN=1;DP=1245;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.98;SOR=1.811 GT:AD:DP:GQ:PL 1:0,1221:1221:99:40281,0 -MN908947.3 2453 . C T 26781.04 . AC=1;AF=1.00;AN=1;DP=792;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.86;SOR=2.074 GT:AD:DP:GQ:PL 1:0,791:791:99:26791,0 -MN908947.3 3037 . C T 47212.04 . AC=1;AF=1.00;AN=1;DP=1474;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.76;SOR=1.446 GT:AD:DP:GQ:PL 1:0,1441:1441:99:47222,0 -MN908947.3 3267 . C T 57382.04 . AC=1;AF=1.00;AN=1;DP=1636;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.01;QD=29.76;SOR=2.279 GT:AD:DP:GQ:PL 1:0,1618:1618:99:57392,0 -MN908947.3 4891 . C T 30228.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.156;DP=893;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.19;ReadPosRankSum=0.853;SOR=1.032 GT:AD:DP:GQ:PL 1:1,883:884:99:30238,0 -MN908947.3 5388 . C A 35005.04 . AC=1;AF=1.00;AN=1;DP=988;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.91;SOR=2.589 GT:AD:DP:GQ:PL 1:0,981:981:99:35015,0 -MN908947.3 5986 . C T 27793.04 . AC=1;AF=1.00;AN=1;DP=778;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=25.60;SOR=2.610 GT:AD:DP:GQ:PL 1:0,776:776:99:27803,0 -MN908947.3 6322 . T A 46183.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.395;DP=1454;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.01;MQRankSum=0.056;QD=31.85;ReadPosRankSum=-0.308;SOR=0.638 GT:AD:DP:GQ:PL 1:1,1449:1450:99:46193,0 -MN908947.3 6954 . T C 15609.04 . AC=1;AF=1.00;AN=1;DP=470;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.16;SOR=2.116 GT:AD:DP:GQ:PL 1:0,457:457:99:15619,0 -MN908947.3 9163 . C T 52449.04 . AC=1;AF=1.00;AN=1;DP=1567;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.64;SOR=1.933 GT:AD:DP:GQ:PL 1:0,1559:1559:99:52459,0 -MN908947.3 11287 . GTCTGGTTTT G 85929.01 . AC=1;AF=1.00;AN=1;DP=1987;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.16;QD=29.45;SOR=2.296 GT:AD:DP:GQ:PL 1:0,1921:1921:99:85939,0 -MN908947.3 14408 . C T 43957.04 . AC=1;AF=1.00;AN=1;DP=1376;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.98;SOR=0.877 GT:AD:DP:GQ:PL 1:0,1333:1333:99:43967,0 -MN908947.3 14676 . C T 59038.04 . AC=1;AF=1.00;AN=1;DP=1722;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.57;SOR=1.911 GT:AD:DP:GQ:PL 1:0,1708:1708:99:59048,0 -MN908947.3 15279 . C T 33241.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.031;DP=982;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.16;ReadPosRankSum=1.653;SOR=1.221 GT:AD:DP:GQ:PL 1:1,972:973:99:33251,0 -MN908947.3 16176 . T C 28038.04 . AC=1;AF=1.00;AN=1;DP=828;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.57;SOR=0.829 GT:AD:DP:GQ:PL 1:0,767:767:99:28048,0 -MN908947.3 21764 . ATACATG A 39465.01 . AC=1;AF=1.00;AN=1;DP=948;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.33;QD=27.80;SOR=1.881 GT:AD:DP:GQ:PL 1:0,888:888:99:39475,0 -MN908947.3 21990 . TTTA T 19462.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.920;DP=615;FS=8.586;MLEAC=1;MLEAF=1.00;MQ=60.23;MQRankSum=0.320;QD=33.50;ReadPosRankSum=3.705;SOR=1.108 GT:AD:DP:GQ:PL 1:7,574:581:99:19472,0 -MN908947.3 23063 . A T 914.04 . AC=1;AF=1.00;AN=1;DP=26;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=22.38;SOR=1.697 GT:AD:DP:GQ:PL 1:0,26:26:99:924,0 -MN908947.3 23271 . C A 52949.04 . AC=1;AF=1.00;AN=1;DP=1606;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.01;QD=33.30;SOR=1.881 GT:AD:DP:GQ:PL 1:0,1590:1590:99:52959,0 -MN908947.3 23403 . A G 52459.04 . AC=1;AF=1.00;AN=1;DP=1550;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.35;SOR=1.548 GT:AD:DP:GQ:PL 1:0,1527:1527:99:52469,0 -MN908947.3 23604 . C A 45289.04 . AC=1;AF=1.00;AN=1;DP=1343;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.13;SOR=1.418 GT:AD:DP:GQ:PL 1:0,1327:1327:99:45299,0 -MN908947.3 23709 . C T 48176.04 . AC=1;AF=1.00;AN=1;DP=1453;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.39;SOR=2.563 GT:AD:DP:GQ:PL 1:0,1443:1443:99:48186,0 -MN908947.3 24506 . T G 26859.04 . AC=1;AF=1.00;AN=1;DP=727;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=25.88;SOR=3.103 GT:AD:DP:GQ:PL 1:0,722:722:99:26869,0 -MN908947.3 24914 . G C 74535.04 . AC=1;AF=1.00;AN=1;DP=2283;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.48;SOR=2.128 GT:AD:DP:GQ:PL 1:0,2226:2226:99:74545,0 -MN908947.3 27972 . C T 34532.04 . AC=1;AF=1.00;AN=1;DP=1128;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.34;SOR=0.768 GT:AD:DP:GQ:PL 1:0,1102:1102:99:34542,0 -MN908947.3 28048 . G T 31255.04 . AC=1;AF=1.00;AN=1;DP=952;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.83;SOR=1.823 GT:AD:DP:GQ:PL 1:0,952:952:99:31265,0 -MN908947.3 28111 . A G 34678.04 . AC=1;AF=1.00;AN=1;DP=1015;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=24.89;SOR=0.897 GT:AD:DP:GQ:PL 1:0,964:964:99:34688,0 -MN908947.3 28270 . TA T 55816.04 . AC=1;AF=1.00;AN=1;DP=1680;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=34.99;SOR=0.736 GT:AD:DP:GQ:PL 1:0,1595:1595:99:70334,0 -MN908947.3 28280 . G C 50509.04 . AC=1;AF=1.00;AN=1;DP=1528;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=33.12;SOR=0.834 GT:AD:DP:GQ:PL 1:0,1525:1525:99:67590,0 -MN908947.3 28281 . A T 49920.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=2.102;DP=1533;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;MQRankSum=-0.087;QD=33.94;ReadPosRankSum=0.058;SOR=0.727 GT:AD:DP:GQ:PL 1:13,1458:1471:99:49930,0 -MN908947.3 28282 . T A 67409.04 . AC=1;AF=1.00;AN=1;DP=1543;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=30.11;SOR=0.834 GT:AD:DP:GQ:PL 1:0,1520:1520:99:67419,0 -MN908947.3 28881 . G A 31138.04 . AC=1;AF=1.00;AN=1;DP=708;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.18;SOR=0.971 GT:AD:DP:GQ:PL 1:0,696:696:99:31148,0 -MN908947.3 28882 . G A 31138.04 . AC=1;AF=1.00;AN=1;DP=706;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.68;SOR=0.971 GT:AD:DP:GQ:PL 1:0,696:696:99:31148,0 -MN908947.3 28883 . G C 31138.04 . AC=1;AF=1.00;AN=1;DP=722;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.93;SOR=0.971 GT:AD:DP:GQ:PL 1:0,696:696:99:31148,0 -MN908947.3 28977 . C T 16071.04 . AC=1;AF=1.00;AN=1;DP=462;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.80;SOR=3.307 GT:AD:DP:GQ:PL 1:0,427:427:99:16081,0 -MN908947.3 29861 . G GTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATT 119.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.060;DP=12;FS=13.222;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=17.00;ReadPosRankSum=-0.366;SOR=3.587 GT:AD:DP:GQ:PL 1:2,5:7:99:129,0 diff --git a/benchmark/ERR5397623/ERR5397623.preprocessed.ivar.tsv b/benchmark/ERR5397623/ERR5397623.preprocessed.ivar.tsv deleted file mode 100644 index 7b50fd1..0000000 --- a/benchmark/ERR5397623/ERR5397623.preprocessed.ivar.tsv +++ /dev/null @@ -1,68 +0,0 @@ -REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA -MN908947.3 186 C T 517 4 49 19 0 50 0.0354478 536 9.98009e-08 TRUE NA NA NA NA NA -MN908947.3 241 C T 0 0 0 521 154 53 1 521 0 TRUE NA NA NA NA NA -MN908947.3 277 T C 0 0 0 504 273 48 1 504 0 TRUE CDS:ENSSASP00005000003 CTT L CTC L -MN908947.3 277 T C 0 0 0 504 273 48 1 504 0 TRUE CDS:ENSSASP00005000002 CTT L CTC L -MN908947.3 417 G C 557 69 47 21 0 48 0.0363322 578 3.3e-08 TRUE CDS:ENSSASP00005000003 TGT C TCT S -MN908947.3 417 G C 557 69 47 21 0 48 0.0363322 578 3.3e-08 TRUE CDS:ENSSASP00005000002 TGT C TCT S -MN908947.3 913 C T 0 0 0 947 550 53 1 947 0 TRUE CDS:ENSSASP00005000003 TCC S TCT S -MN908947.3 913 C T 0 0 0 947 550 53 1 947 0 TRUE CDS:ENSSASP00005000002 TCC S TCT S -MN908947.3 2453 C T 1 1 39 622 405 50 0.998395 623 0 TRUE CDS:ENSSASP00005000003 CTC L TTC F -MN908947.3 2453 C T 1 1 39 622 405 50 0.998395 623 0 TRUE CDS:ENSSASP00005000002 CTC L TTC F -MN908947.3 3037 C T 0 0 0 1052 534 53 1 1052 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 3037 C T 0 0 0 1052 534 53 1 1052 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 3267 C T 0 0 0 1365 29 49 1 1365 0 TRUE CDS:ENSSASP00005000003 ACT T ATT I -MN908947.3 3267 C T 0 0 0 1365 29 49 1 1365 0 TRUE CDS:ENSSASP00005000002 ACT T ATT I -MN908947.3 4891 C T 1 1 37 679 440 50 0.998529 680 0 TRUE CDS:ENSSASP00005000003 ACC T ACT T -MN908947.3 4891 C T 1 1 37 679 440 50 0.998529 680 0 TRUE CDS:ENSSASP00005000002 ACC T ACT T -MN908947.3 5388 C A 0 0 0 800 16 47 1 800 0 TRUE CDS:ENSSASP00005000003 GCT A GAT D -MN908947.3 5388 C A 0 0 0 800 16 47 1 800 0 TRUE CDS:ENSSASP00005000002 GCT A GAT D -MN908947.3 5986 C T 0 0 0 654 13 48 1 654 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 5986 C T 0 0 0 654 13 48 1 654 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 6322 T A 1 0 39 1061 13 56 0.999058 1062 0 TRUE CDS:ENSSASP00005000003 GTT V GTA V -MN908947.3 6322 T A 1 0 39 1061 13 56 0.999058 1062 0 TRUE CDS:ENSSASP00005000002 GTT V GTA V -MN908947.3 6638 C T 1226 261 53 49 15 55 0.0384314 1275 1.69845e-19 TRUE CDS:ENSSASP00005000003 CAT H TAT Y -MN908947.3 6638 C T 1226 261 53 49 15 55 0.0384314 1275 1.69845e-19 TRUE CDS:ENSSASP00005000002 CAT H TAT Y -MN908947.3 6954 T C 0 0 0 345 223 50 1 345 3.36866e-237 TRUE CDS:ENSSASP00005000003 ATA I ACA T -MN908947.3 6954 T C 0 0 0 345 223 50 1 345 3.36866e-237 TRUE CDS:ENSSASP00005000002 ATA I ACA T -MN908947.3 7613 T G 598 432 48 21 13 50 0.0339257 619 2.67592e-08 TRUE CDS:ENSSASP00005000003 TGG W GGG G -MN908947.3 7613 T G 598 432 48 21 13 50 0.0339257 619 2.67592e-08 TRUE CDS:ENSSASP00005000002 TGG W GGG G -MN908947.3 9163 C T 0 0 0 1222 758 50 1 1222 0 TRUE CDS:ENSSASP00005000003 AAC N AAT N -MN908947.3 9163 C T 0 0 0 1222 758 50 1 1222 0 TRUE CDS:ENSSASP00005000002 AAC N AAT N -MN908947.3 11027 T C 767 139 44 40 0 41 0.0495663 807 1.23681e-14 TRUE CDS:ENSSASP00005000003 TTG L CTG L -MN908947.3 11027 T C 767 139 44 40 0 41 0.0495663 807 1.23681e-14 TRUE CDS:ENSSASP00005000002 TTG L CTG L -MN908947.3 11287 G -NNNNNNNNN 1715 1190 50 2094 0 20 0.933155 2244 0 TRUE NA NA NA NA NA -MN908947.3 13668 T C 330 25 45 12 0 35 0.0350877 342 6.09239e-05 TRUE CDS:ENSSASP00005000002 CTT L CCT P -MN908947.3 14408 C T 1 1 20 980 256 52 0.998981 981 0 TRUE CDS:ENSSASP00005000002 CTA L TTA L -MN908947.3 14676 C T 0 0 0 1410 47 52 1 1410 0 TRUE CDS:ENSSASP00005000002 CCG P CTG L -MN908947.3 15168 G A 129 97 35 6 6 22 0.0444444 135 0.0247848 FALSE CDS:ENSSASP00005000002 TGA * TAA * -MN908947.3 15279 C T 1 0 35 759 2 50 0.997372 761 0 TRUE CDS:ENSSASP00005000002 ACC T ATC I -MN908947.3 16176 T C 0 0 0 701 341 43 1 701 0 TRUE CDS:ENSSASP00005000002 CTT L CCT P -MN908947.3 19549 G A 50 36 41 2 2 31 0.0384615 52 0.209545 FALSE CDS:ENSSASP00005000002 CAG Q CAA Q -MN908947.3 20091 C T 201 133 47 7 6 40 0.0336538 208 0.001947 TRUE CDS:ENSSASP00005000002 CCA P CTA L -MN908947.3 21667 T G 308 178 45 16 0 32 0.0493827 324 1.96287e-06 TRUE CDS:ENSSASP00005000004 GGT G GGG G -MN908947.3 21764 A -NNNNNN 718 7 51 966 0 20 0.980711 985 5.74572e-241 TRUE NA NA NA NA NA -MN908947.3 21990 T -NNN 482 284 44 500 0 20 0.851789 587 2.70973e-121 TRUE NA NA NA NA NA -MN908947.3 22088 C T 471 23 48 25 0 53 0.0504032 496 7.75717e-10 TRUE CDS:ENSSASP00005000004 CTT L TTT F -MN908947.3 22452 C -N 48 10 51 2 0 20 0.03125 64 0.193584 FALSE NA NA NA NA NA -MN908947.3 23063 A T 0 0 0 21 13 46 1 21 1.44019e-13 TRUE CDS:ENSSASP00005000004 AAT N TAT Y -MN908947.3 23099 C +T 16 9 47 2 0 20 0.1 20 0.22973 FALSE NA NA NA NA NA -MN908947.3 23271 C A 0 0 0 1235 2 54 1 1235 0 TRUE CDS:ENSSASP00005000004 GCT A GAT D -MN908947.3 23403 A G 0 0 0 1268 725 52 1 1268 0 TRUE CDS:ENSSASP00005000004 GAT D GGT G -MN908947.3 23604 C A 0 0 0 1122 107 50 1 1122 0 TRUE CDS:ENSSASP00005000004 CCT P CAT H -MN908947.3 23709 C T 0 0 0 1142 741 49 1 1142 0 TRUE CDS:ENSSASP00005000004 ACA T ATA I -MN908947.3 24506 T G 0 0 0 650 3 45 1 650 0 TRUE CDS:ENSSASP00005000004 TCA S GCA A -MN908947.3 24914 G C 0 0 0 1799 1167 49 1 1799 0 TRUE CDS:ENSSASP00005000004 GAC D CAC H -MN908947.3 25603 C T 917 693 46 37 33 39 0.0387841 954 1.92005e-12 TRUE CDS:ENSSASP00005000006 CTA L TTA L -MN908947.3 27540 A G 24 1 47 1 0 39 0.04 25 0.446429 FALSE CDS:ENSSASP00005000009 CTA L CTG L -MN908947.3 27972 C T 0 0 0 761 217 56 1 761 0 TRUE CDS:ENSSASP00005000008 CAA Q TAA * -MN908947.3 28048 G T 0 0 0 694 400 53 1 694 0 TRUE CDS:ENSSASP00005000008 AGA R ATA I -MN908947.3 28111 A G 0 0 0 913 263 44 1 913 0 TRUE CDS:ENSSASP00005000008 TAC Y TGC C -MN908947.3 28270 T -N 1348 343 52 1563 0 20 0.844865 1850 0 TRUE NA NA NA NA NA -MN908947.3 28280 G C 0 0 0 1145 438 49 0.996519 1149 0 TRUE CDS:ENSSASP00005000005 GAT D CAT H -MN908947.3 28281 A T 7 1 60 1148 447 48 0.99308 1156 0 TRUE CDS:ENSSASP00005000005 GAT D GTT V -MN908947.3 28282 T A 0 0 0 1189 475 49 1 1189 0 TRUE CDS:ENSSASP00005000005 GAT D GAA E -MN908947.3 28881 G A 0 0 0 469 196 48 1 469 0 TRUE CDS:ENSSASP00005000005 AGG R AAG K -MN908947.3 28882 G A 0 0 0 467 193 47 1 467 0 TRUE CDS:ENSSASP00005000005 AGG R AGA R -MN908947.3 28883 G C 0 0 0 477 201 48 1 477 0 TRUE CDS:ENSSASP00005000005 GGA G CGA R -MN908947.3 28977 C T 0 0 0 394 308 44 1 394 6.14061e-256 TRUE CDS:ENSSASP00005000005 TCT S TTT F diff --git a/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter01.vcf b/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter01.vcf deleted file mode 100644 index c995381..0000000 --- a/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter01.vcf +++ /dev/null @@ -1,58 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5397623/ERR5397623.preprocessed.lofreq.vcf ERR5397623/ERR5397623.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.1' ./ERR5397623/ERR5397623.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:38 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 26633 PASS DP=759;AF=0.981555;SB=0;DP4=0,0,370,388 -MN908947.3 277 . T C 24097 PASS DP=649;AF=0.987673;SB=0;DP4=0,0,233,415 -MN908947.3 913 . C T 49314 PASS DP=1331;AF=0.990233;SB=0;DP4=0,0,397,933 -MN908947.3 2453 . C T 31244 PASS DP=844;AF=0.978673;SB=0;DP4=0,1,219,623 -MN908947.3 3037 . C T 49314 PASS DP=1468;AF=0.984332;SB=0;DP4=0,0,518,949 -MN908947.3 3267 . C T 49314 PASS DP=1747;AF=0.987979;SB=0;DP4=0,0,1330,415 -MN908947.3 4891 . C T 33820 PASS DP=899;AF=0.993326;SB=0;DP4=0,1,239,659 -MN908947.3 5388 . C A 37876 PASS DP=1009;AF=0.986125;SB=0;DP4=0,0,793,216 -MN908947.3 5986 . C T 30691 PASS DP=820;AF=0.993902;SB=0;DP4=0,0,644,175 -MN908947.3 6322 . T A 49314 PASS DP=1558;AF=0.98973;SB=0;DP4=1,0,1051,506 -MN908947.3 6954 . T C 16932 PASS DP=457;AF=0.986871;SB=0;DP4=0,0,122,335 -MN908947.3 9163 . C T 49314 PASS DP=1634;AF=0.982252;SB=0;DP4=0,0,464,1170 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=2093;AF=1;SB=3;DP4=39,110,487,1606;INDEL;HRUN=1 -MN908947.3 14408 . C T 49314 PASS DP=1358;AF=0.986745;SB=3;DP4=0,1,727,630 -MN908947.3 14676 . C T 49314 PASS DP=1922;AF=0.993757;SB=0;DP4=0,0,1367,555 -MN908947.3 15279 . C T 36533 PASS DP=1002;AF=0.98503;SB=0;DP4=1,0,760,239 -MN908947.3 16176 . T C 30080 PASS DP=826;AF=0.990315;SB=0;DP4=0,0,362,464 -MN908947.3 21764 . ATACATG A 35010 PASS DP=985;AF=0.980711;SB=30;DP4=7,12,710,256;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 18675 PASS DP=580;AF=0.862069;SB=24;DP4=17,66,184,316;INDEL;HRUN=3 -MN908947.3 23063 . A T 948 PASS DP=26;AF=0.961538;SB=0;DP4=0,0,8,18 -MN908947.3 23099 . C CT 64 PASS DP=18;AF=0.111111;SB=0;DP4=6,12,1,1;INDEL;HRUN=3 -MN908947.3 23271 . C A 49314 PASS DP=1743;AF=0.984509;SB=0;DP4=0,0,1230,513 -MN908947.3 23403 . A G 49314 PASS DP=1740;AF=0.983908;SB=0;DP4=0,0,545,1195 -MN908947.3 23604 . C A 49314 PASS DP=1512;AF=0.986772;SB=0;DP4=0,0,1020,492 -MN908947.3 23709 . C T 49314 PASS DP=1553;AF=0.918867;SB=29;DP4=5,0,402,1145 -MN908947.3 24506 . T G 29296 PASS DP=783;AF=0.985951;SB=0;DP4=0,0,653,130 -MN908947.3 24914 . G C 49314 PASS DP=2377;AF=0.991165;SB=0;DP4=0,0,634,1742 -MN908947.3 27972 . C T 42186 PASS DP=1130;AF=0.980531;SB=0;DP4=0,0,546,583 -MN908947.3 28048 . G T 36713 PASS DP=970;AF=0.984536;SB=0;DP4=0,0,295,674 -MN908947.3 28111 . A G 39804 PASS DP=1116;AF=0.983871;SB=0;DP4=0,0,658,458 -MN908947.3 28270 . TA T 33844 PASS DP=1833;AF=0.844517;SB=115;DP4=212,75,804,744;INDEL;HRUN=4 -MN908947.3 28280 . G C 31151 PASS DP=1456;AF=0.98489;SB=0;DP4=0,0,713,739 -MN908947.3 28281 . A T 30994 PASS DP=1456;AF=0.983516;SB=2;DP4=7,5,705,737 -MN908947.3 28282 . T A 32298 PASS DP=1510;AF=0.99404;SB=0;DP4=0,0,719,790 -MN908947.3 28881 . G A 21845 PASS DP=581;AF=0.982788;SB=0;DP4=0,0,253,328 -MN908947.3 28882 . G A 21234 PASS DP=581;AF=0.974182;SB=0;DP4=0,0,253,328 -MN908947.3 28883 . G C 21883 PASS DP=590;AF=0.986441;SB=0;DP4=0,0,253,337 -MN908947.3 28977 . C T 17221 PASS DP=462;AF=0.980519;SB=0;DP4=0,0,86,376 diff --git a/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter02.vcf b/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter02.vcf deleted file mode 100644 index 9a7cebc..0000000 --- a/benchmark/ERR5397623/ERR5397623.preprocessed.lofreq.vcf.filter02.vcf +++ /dev/null @@ -1,57 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5397623/ERR5397623.preprocessed.lofreq.vcf ERR5397623/ERR5397623.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' ./ERR5397623/ERR5397623.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:38 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 26633 PASS DP=759;AF=0.981555;SB=0;DP4=0,0,370,388 -MN908947.3 277 . T C 24097 PASS DP=649;AF=0.987673;SB=0;DP4=0,0,233,415 -MN908947.3 913 . C T 49314 PASS DP=1331;AF=0.990233;SB=0;DP4=0,0,397,933 -MN908947.3 2453 . C T 31244 PASS DP=844;AF=0.978673;SB=0;DP4=0,1,219,623 -MN908947.3 3037 . C T 49314 PASS DP=1468;AF=0.984332;SB=0;DP4=0,0,518,949 -MN908947.3 3267 . C T 49314 PASS DP=1747;AF=0.987979;SB=0;DP4=0,0,1330,415 -MN908947.3 4891 . C T 33820 PASS DP=899;AF=0.993326;SB=0;DP4=0,1,239,659 -MN908947.3 5388 . C A 37876 PASS DP=1009;AF=0.986125;SB=0;DP4=0,0,793,216 -MN908947.3 5986 . C T 30691 PASS DP=820;AF=0.993902;SB=0;DP4=0,0,644,175 -MN908947.3 6322 . T A 49314 PASS DP=1558;AF=0.98973;SB=0;DP4=1,0,1051,506 -MN908947.3 6954 . T C 16932 PASS DP=457;AF=0.986871;SB=0;DP4=0,0,122,335 -MN908947.3 9163 . C T 49314 PASS DP=1634;AF=0.982252;SB=0;DP4=0,0,464,1170 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=2093;AF=1;SB=3;DP4=39,110,487,1606;INDEL;HRUN=1 -MN908947.3 14408 . C T 49314 PASS DP=1358;AF=0.986745;SB=3;DP4=0,1,727,630 -MN908947.3 14676 . C T 49314 PASS DP=1922;AF=0.993757;SB=0;DP4=0,0,1367,555 -MN908947.3 15279 . C T 36533 PASS DP=1002;AF=0.98503;SB=0;DP4=1,0,760,239 -MN908947.3 16176 . T C 30080 PASS DP=826;AF=0.990315;SB=0;DP4=0,0,362,464 -MN908947.3 21764 . ATACATG A 35010 PASS DP=985;AF=0.980711;SB=30;DP4=7,12,710,256;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 18675 PASS DP=580;AF=0.862069;SB=24;DP4=17,66,184,316;INDEL;HRUN=3 -MN908947.3 23063 . A T 948 PASS DP=26;AF=0.961538;SB=0;DP4=0,0,8,18 -MN908947.3 23271 . C A 49314 PASS DP=1743;AF=0.984509;SB=0;DP4=0,0,1230,513 -MN908947.3 23403 . A G 49314 PASS DP=1740;AF=0.983908;SB=0;DP4=0,0,545,1195 -MN908947.3 23604 . C A 49314 PASS DP=1512;AF=0.986772;SB=0;DP4=0,0,1020,492 -MN908947.3 23709 . C T 49314 PASS DP=1553;AF=0.918867;SB=29;DP4=5,0,402,1145 -MN908947.3 24506 . T G 29296 PASS DP=783;AF=0.985951;SB=0;DP4=0,0,653,130 -MN908947.3 24914 . G C 49314 PASS DP=2377;AF=0.991165;SB=0;DP4=0,0,634,1742 -MN908947.3 27972 . C T 42186 PASS DP=1130;AF=0.980531;SB=0;DP4=0,0,546,583 -MN908947.3 28048 . G T 36713 PASS DP=970;AF=0.984536;SB=0;DP4=0,0,295,674 -MN908947.3 28111 . A G 39804 PASS DP=1116;AF=0.983871;SB=0;DP4=0,0,658,458 -MN908947.3 28270 . TA T 33844 PASS DP=1833;AF=0.844517;SB=115;DP4=212,75,804,744;INDEL;HRUN=4 -MN908947.3 28280 . G C 31151 PASS DP=1456;AF=0.98489;SB=0;DP4=0,0,713,739 -MN908947.3 28281 . A T 30994 PASS DP=1456;AF=0.983516;SB=2;DP4=7,5,705,737 -MN908947.3 28282 . T A 32298 PASS DP=1510;AF=0.99404;SB=0;DP4=0,0,719,790 -MN908947.3 28881 . G A 21845 PASS DP=581;AF=0.982788;SB=0;DP4=0,0,253,328 -MN908947.3 28882 . G A 21234 PASS DP=581;AF=0.974182;SB=0;DP4=0,0,253,328 -MN908947.3 28883 . G C 21883 PASS DP=590;AF=0.986441;SB=0;DP4=0,0,253,337 -MN908947.3 28977 . C T 17221 PASS DP=462;AF=0.980519;SB=0;DP4=0,0,86,376 diff --git a/benchmark/ERR5397623/ERR5397623.vcf b/benchmark/ERR5397623/ERR5397623.vcf deleted file mode 100644 index db7d47d..0000000 --- a/benchmark/ERR5397623/ERR5397623.vcf +++ /dev/null @@ -1,66 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5397623/ERR5397623.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5397623.vcf; Date=Mon Jun 7 15:52:25 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=107;VDB=0.631715;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,32;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 277 . T C 225.417 . DP=105;VDB=0.301872;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,42;MQ=60 GT:PL:AD 1:255,0:0,101 -MN908947.3 913 . C T 225.417 . DP=95;VDB=0.0116183;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,29;MQ=60 GT:PL:AD 1:255,0:0,90 -MN908947.3 2453 . C T 225.417 . DP=99;VDB=0.726511;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,48,48;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 3037 . C T 225.422 . DP=112;VDB=0.047627;SGB=-0.693147;MQSB=0.979803;MQ0F=0;AC=1;AN=1;DP4=0,0,62,43;MQ=59 GT:PL:AD 1:255,0:0,104 -MN908947.3 3267 . C T 225.417 . DP=104;VDB=0.728207;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,18;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 4891 . C T 228.405 . DP=104;VDB=0.413458;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,49;MQ=60 GT:PL:AD 1:255,0:1,96 -MN908947.3 5388 . C A 225.417 . DP=96;VDB=0.132707;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,19;MQ=60 GT:PL:AD 1:255,0:0,86 -MN908947.3 5986 . C T 225.417 . DP=83;VDB=0.0647342;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,16;MQ=60 GT:PL:AD 1:255,0:0,79 -MN908947.3 6322 . T A 225.417 . DP=102;VDB=0.367309;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,71,27;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 6954 . T C 225.417 . DP=90;VDB=0.201374;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,44;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 9163 . C T 225.417 . DP=106;VDB=0.102543;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,56,34;MQ=60 GT:PL:AD 1:255,0:0,90 -MN908947.3 11287 . GTCTGGTTTT G 228.408 . INDEL;IDV=104;IMF=0.962963;DP=108;VDB=0.000667777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,71,30;MQ=60 GT:PL:AD 1:255,0:7,101 -MN908947.3 14408 . C T 225.417 . DP=106;VDB=0.249649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,32;MQ=60 GT:PL:AD 1:255,0:0,99 -MN908947.3 14676 . C T 225.417 . DP=121;VDB=0.107184;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 15279 . C T 225.417 . DP=83;VDB=0.0200448;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,15;MQ=60 GT:PL:AD 1:255,0:0,75 -MN908947.3 16176 . T C 225.417 . DP=72;VDB=0.999978;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,17;MQ=60 GT:PL:AD 1:255,0:0,63 -MN908947.3 21764 . ATACATGT AT 228.36 . INDEL;IDV=71;IMF=0.946667;DP=75;VDB=0.00709019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,2,51,20;MQ=60 GT:PL:AD 1:255,0:4,71 -MN908947.3 21990 . TTTATTA TTTA 141.204 . INDEL;IDV=48;IMF=0.8;DP=60;VDB=0.999506;SGB=-0.693147;MQSB=0.986846;MQ0F=0;AC=1;AN=1;DP4=5,8,34,13;MQ=59 GT:PL:AD 1:255,87:13,47 -MN908947.3 21991 . TTAT TT 97.7941 . INDEL;IDV=1;IMF=0.0175439;DP=57;VDB=0.999337;SGB=-0.69311;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=17,9,20,11;MQ=60 GT:PL:AD 1:183,58:26,31 -MN908947.3 23063 . A T 225.417 . DP=19;VDB=0.970247;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,6,12;MQ=60 GT:PL:AD 1:255,0:0,18 -MN908947.3 23271 . C A 225.417 . DP=120;VDB=0.849019;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,27;MQ=60 GT:PL:AD 1:255,0:0,117 -MN908947.3 23403 . A G 225.417 . DP=116;VDB=0.255022;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,30;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 23604 . C A 225.417 . DP=102;VDB=0.122654;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,24;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 23709 . C T 225.417 . DP=105;VDB=0.00948335;SGB=-0.693147;MQSB=0.990148;MQ0F=0.00952381;AC=1;AN=1;DP4=0,0,60,40;MQ=59 GT:PL:AD 1:255,0:0,100 -MN908947.3 24506 . T G 225.417 . DP=77;VDB=0.00632777;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,14;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.827713;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,65,45;MQ=60 GT:PL:AD 1:255,0:0,110 -MN908947.3 27972 . C T 225.417 . DP=104;VDB=0.903335;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,38;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 28048 . G T 225.417 . DP=97;VDB=0.339895;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,46,43;MQ=60 GT:PL:AD 1:255,0:0,89 -MN908947.3 28111 . A G 225.417 . DP=78;VDB=0.815;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,47,23;MQ=60 GT:PL:AD 1:255,0:0,70 -MN908947.3 28270 . TAAAA TAAA 9.28705 . INDEL;IDV=91;IMF=0.858491;DP=106;VDB=0.741118;SGB=-0.693147;MQSB=0.993956;MQ0F=0;AC=1;AN=1;DP4=19,10,55,22;MQ=59 GT:PL:AD 1:113,77:29,77 -MN908947.3 28280 . G C 225.417 . DP=91;VDB=0.0245211;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59 GT:PL:AD 1:255,0:0,88 -MN908947.3 28281 . A T 228.367 . DP=91;VDB=0.0109476;SGB=-0.693147;RPB=0.836342;MQB=0.620315;MQSB=0.992166;BQB=0.299824;MQ0F=0;AC=1;AN=1;DP4=2,1,58,27;MQ=59 GT:PL:AD 1:255,0:3,85 -MN908947.3 28282 . T A 225.417 . DP=92;VDB=0.0227728;SGB=-0.693147;MQSB=0.992166;MQ0F=0;AC=1;AN=1;DP4=0,0,60,28;MQ=59 GT:PL:AD 1:255,0:0,88 -MN908947.3 28881 . G A 225.422 . DP=98;VDB=0.0635294;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,94 -MN908947.3 28882 . G A 225.417 . DP=98;VDB=0.0651209;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,95 -MN908947.3 28883 . G C 225.417 . DP=99;VDB=0.0583443;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,36;MQ=60 GT:PL:AD 1:255,0:0,95 -MN908947.3 28977 . C T 225.417 . DP=63;VDB=0.004806;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,29;MQ=60 GT:PL:AD 1:255,0:0,60 diff --git a/benchmark/ERR5401235/ERR5401235.annotated.vcf b/benchmark/ERR5401235/ERR5401235.annotated.vcf deleted file mode 100644 index 2d3daa3..0000000 --- a/benchmark/ERR5401235/ERR5401235.annotated.vcf +++ /dev/null @@ -1,82 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5401235/ERR5401235.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5401235.vcf; Date=Mon Jun 7 15:54:45 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:54:57 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5401235.normalized.vcf -; Date=Mon Jun 7 15:54:57 2021 -##bcftools/csqVersion=1.12+htslib-1.12 -##bcftools/csqCommand=csq --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --gff-annot /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.101.gff3 -o ERR5401235.annotated.vcf /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5401235/ERR5401235.normalized.vcf; Date=Mon Jun 7 15:54:58 2021 -##INFO= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=109;VDB=0.73659;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,37;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 913 . C T 225.417 . DP=102;VDB=0.059221;SGB=-0.693147;MQSB=0.992652;MQ0F=0;AC=1;AN=1;DP4=0,0,65,31;MQ=59;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|216S|913C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|216S|913C>T GT:PL:AD:BCSQ 1:255,0:0,96:5 -MN908947.3 1968 . C T 225.417 . DP=57;VDB=0.18868;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,35,14;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|568T>568I|1968C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|568T>568I|1968C>T GT:PL:AD:BCSQ 1:255,0:0,49:5 -MN908947.3 2761 . A G 225.417 . DP=84;VDB=0.524286;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,41;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|832E|2761A>G,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|832E|2761A>G GT:PL:AD:BCSQ 1:255,0:0,77:5 -MN908947.3 3037 . C T 225.417 . DP=94;VDB=0.666921;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,35;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|924F|3037C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|924F|3037C>T GT:PL:AD:BCSQ 1:255,0:0,85:5 -MN908947.3 3267 . C T 225.417 . DP=105;VDB=0.185938;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,81,17;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1001T>1001I|3267C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1001T>1001I|3267C>T GT:PL:AD:BCSQ 1:255,0:0,98:5 -MN908947.3 5388 . C A 225.417 . DP=88;VDB=0.109619;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,22;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1708A>1708D|5388C>A,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1708A>1708D|5388C>A GT:PL:AD:BCSQ 1:255,0:0,84:5 -MN908947.3 5986 . C T 225.417 . DP=84;VDB=0.159577;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,18;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1907F|5986C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1907F|5986C>T GT:PL:AD:BCSQ 1:255,0:0,77:5 -MN908947.3 6954 . T C 225.417 . DP=85;VDB=0.519512;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,38;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2230I>2230T|6954T>C,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2230I>2230T|6954T>C GT:PL:AD:BCSQ 1:255,0:0,78:5 -MN908947.3 7675 . G T 175.17 . DP=51;VDB=9.90477e-09;SGB=-0.693146;RPB=0.0094;MQB=1;MQSB=1;BQB=0.767974;MQ0F=0;AC=1;AN=1;DP4=3,2,39,5;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|2470A|7675G>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|2470A|7675G>T GT:PL:AD:BCSQ 1:244,42:5,44:5 -MN908947.3 10329 . A G 225.417 . DP=114;VDB=0.37684;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,43;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|3355D>3355G|10329A>G,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|3355D>3355G|10329A>G GT:PL:AD:BCSQ 1:255,0:0,103:5 -MN908947.3 11287 . GTCTGGTTTT G 228.365 . INDEL;IDV=96;IMF=0.941176;DP=102;VDB=0.00658878;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=5,7,61,29;MQ=60;BCSQ=inframe_deletion|ORF1ab|ENSSAST00005000003|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G,inframe_deletion|ORF1ab|ENSSAST00005000002|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G GT:PL:AD:BCSQ 1:255,0:12,90:5 -MN908947.3 11296 . T G 36.4154 . DP=5;VDB=0.036923;SGB=-0.511536;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,2,1;MQ=60 GT:PL:AD 1:66,0:0,3 -MN908947.3 12162 . A G 225.417 . DP=113;VDB=0.533476;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,30;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|3966Q>3963R|12162A>G,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|3966Q>3963R|12162A>G GT:PL:AD:BCSQ 1:255,0:0,105:5 -MN908947.3 14408 . C T 225.417 . DP=105;VDB=0.356839;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,34;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4715L|14408C>T GT:PL:AD:BCSQ 1:255,0:0,97:1 -MN908947.3 14676 . C T 225.417 . DP=105;VDB=0.069958;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,22;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|4804P>4801L|14676C>T GT:PL:AD:BCSQ 1:255,0:0,101:1 -MN908947.3 15279 . C T 225.417 . DP=86;VDB=0.0709772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,16;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5005T>5002I|15279C>T GT:PL:AD:BCSQ 1:255,0:0,76:1 -MN908947.3 16176 . T C 225.417 . DP=66;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,43,14;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5304L>5301P|16176T>C GT:PL:AD:BCSQ 1:255,0:0,57:1 -MN908947.3 17615 . A G 225.417 . DP=107;VDB=0.522782;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,42;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5784S>5781G|17615A>G GT:PL:AD:BCSQ 1:255,0:0,100:1 -MN908947.3 21762 . CTATACA C 228.402 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00293609;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,7,56,12;MQ=60;OLD_CLUMPED=MN908947.3|21762|CTATACAT|CT;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|67AIH>67A|21762CTATACA>C GT:PL:AD:BCSQ 1:255,0:7,68:1 -MN908947.3 21764 . ATACATG A 228.421 . INDEL;IDV=73;IMF=0.973333;DP=75;VDB=0.00439388;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,3,56,16;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT GT:PL:AD 1:255,0:3,72 -MN908947.3 21766 . ACATGTC A 228.408 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00444089;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,6,54,13;MQ=60 GT:PL:AD 1:255,0:8,67 -MN908947.3 21990 . TTTA T 228.315 . INDEL;IDV=48;IMF=0.842105;DP=57;VDB=0.851606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,5,32,18;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|143VY>141V|21990TTTA>T GT:PL:AD:BCSQ 1:255,0:7,50:1 -MN908947.3 23063 . A T 225.417 . DP=27;VDB=0.974241;SGB=-0.692914;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,7,18;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|501N>498Y|23063A>T GT:PL:AD:BCSQ 1:255,0:0,25:1 -MN908947.3 23271 . C A 225.417 . DP=113;VDB=0.602922;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,87,25;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|570A>567D|23271C>A GT:PL:AD:BCSQ 1:255,0:0,112:1 -MN908947.3 23403 . A G 225.417 . DP=103;VDB=0.311158;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,74,22;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|614D>611G|23403A>G GT:PL:AD:BCSQ 1:255,0:0,96:1 -MN908947.3 23604 . C A 225.417 . DP=103;VDB=0.303274;SGB=-0.693147;MQSB=0.99457;MQ0F=0;AC=1;AN=1;DP4=0,0,71,25;MQ=59;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|681P>678H|23604C>A GT:PL:AD:BCSQ 1:255,0:0,96:1 -MN908947.3 23709 . C T 225.422 . DP=105;VDB=0.072772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,57,46;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|716T>713I|23709C>T GT:PL:AD:BCSQ 1:255,0:0,102:1 -MN908947.3 24506 . T G 225.417 . DP=85;VDB=0.0492644;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,15;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|982S>979A|24506T>G GT:PL:AD:BCSQ 1:255,0:0,81:1 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.741848;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,48;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|1118D>1115H|24914G>C GT:PL:AD:BCSQ 1:255,0:0,114:1 -MN908947.3 25523 . G A 225.417 . DP=117;VDB=0.974641;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,43;MQ=60;BCSQ=missense|ORF3a|ENSSAST00005000006|protein_coding|+|44G>44E|25523G>A GT:PL:AD:BCSQ 1:255,0:0,110:1 -MN908947.3 25693 . C A 225.417 . DP=50;VDB=0.0160805;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,13;MQ=60;BCSQ=missense|ORF3a|ENSSAST00005000006|protein_coding|+|101L>101I|25693C>A GT:PL:AD:BCSQ 1:255,0:0,44:1 -MN908947.3 26606 . C T 225.417 . DP=78;VDB=0.00014612;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,15;MQ=60;BCSQ=synonymous|M|ENSSAST00005000007|protein_coding|+|28F|26606C>T GT:PL:AD:BCSQ 1:255,0:0,74:1 -MN908947.3 27972 . C T 225.417 . DP=111;VDB=0.913367;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,38;MQ=60;BCSQ=stop_gained|ORF8|ENSSAST00005000008|protein_coding|+|27Q>27*|27972C>T GT:PL:AD:BCSQ 1:255,0:0,102:1 -MN908947.3 28048 . G T 225.417 . DP=89;VDB=0.0584099;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,34;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|52R>52I|28048G>T GT:PL:AD:BCSQ 1:255,0:0,84:1 -MN908947.3 28111 . A G 228.412 . DP=77;VDB=0.999359;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,22;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|73Y>73C|28111A>G GT:PL:AD:BCSQ 1:255,0:1,69:1 -MN908947.3 28270 . TA T 5.97268 . INDEL;IDV=90;IMF=0.857143;DP=105;VDB=0.23186;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=20,11,53,21;MQ=60;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:115,83:31,74 -MN908947.3 28280 . G C 225.417 . DP=90;VDB=0.00372887;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|3D>3L|28280G>C+28281A>T+28282T>A GT:PL:AD:BCSQ 1:255,0:0,85:1 -MN908947.3 28281 . A T 225.417 . DP=90;VDB=0.00359238;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,85:1 -MN908947.3 28282 . T A 225.417 . DP=91;VDB=0.00367371;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,85:1 -MN908947.3 28817 . G T 228.414 . DP=75;VDB=0.460414;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,50,16;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|182A>182S|28817G>T GT:PL:AD:BCSQ 1:255,0:1,66:1 -MN908947.3 28881 . G A 225.417 . DP=78;VDB=0.0391523;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|203R>203K|28881G>A+28882G>A GT:PL:AD:BCSQ 1:255,0:0,73:1 -MN908947.3 28882 . G A 225.417 . DP=77;VDB=0.0433548;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60;BCSQ=@28881 GT:PL:AD:BCSQ 1:255,0:0,73:1 -MN908947.3 28883 . G C 225.417 . DP=78;VDB=0.0387719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|204G>204R|28883G>C GT:PL:AD:BCSQ 1:255,0:0,73:1 -MN908947.3 28977 . C T 225.417 . DP=74;VDB=0.318561;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,37;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|235S>235F|28977C>T GT:PL:AD:BCSQ 1:255,0:0,69:1 diff --git a/benchmark/ERR5401235/ERR5401235.normalized.vcf b/benchmark/ERR5401235/ERR5401235.normalized.vcf deleted file mode 100644 index 55bff69..0000000 --- a/benchmark/ERR5401235/ERR5401235.normalized.vcf +++ /dev/null @@ -1,78 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5401235/ERR5401235.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5401235.vcf; Date=Mon Jun 7 15:54:45 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:54:57 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5401235.normalized.vcf -; Date=Mon Jun 7 15:54:57 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=109;VDB=0.73659;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,37;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 913 . C T 225.417 . DP=102;VDB=0.059221;SGB=-0.693147;MQSB=0.992652;MQ0F=0;AC=1;AN=1;DP4=0,0,65,31;MQ=59 GT:PL:AD 1:255,0:0,96 -MN908947.3 1968 . C T 225.417 . DP=57;VDB=0.18868;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,35,14;MQ=60 GT:PL:AD 1:255,0:0,49 -MN908947.3 2761 . A G 225.417 . DP=84;VDB=0.524286;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,41;MQ=60 GT:PL:AD 1:255,0:0,77 -MN908947.3 3037 . C T 225.417 . DP=94;VDB=0.666921;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,35;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 3267 . C T 225.417 . DP=105;VDB=0.185938;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,81,17;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 5388 . C A 225.417 . DP=88;VDB=0.109619;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,22;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 5986 . C T 225.417 . DP=84;VDB=0.159577;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,18;MQ=60 GT:PL:AD 1:255,0:0,77 -MN908947.3 6954 . T C 225.417 . DP=85;VDB=0.519512;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,38;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 7675 . G T 175.17 . DP=51;VDB=9.90477e-09;SGB=-0.693146;RPB=0.0094;MQB=1;MQSB=1;BQB=0.767974;MQ0F=0;AC=1;AN=1;DP4=3,2,39,5;MQ=60 GT:PL:AD 1:244,42:5,44 -MN908947.3 10329 . A G 225.417 . DP=114;VDB=0.37684;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,43;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 11287 . GTCTGGTTTT G 228.365 . INDEL;IDV=96;IMF=0.941176;DP=102;VDB=0.00658878;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=5,7,61,29;MQ=60 GT:PL:AD 1:255,0:12,90 -MN908947.3 11296 . T G 36.4154 . DP=5;VDB=0.036923;SGB=-0.511536;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,2,1;MQ=60 GT:PL:AD 1:66,0:0,3 -MN908947.3 12162 . A G 225.417 . DP=113;VDB=0.533476;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,30;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 14408 . C T 225.417 . DP=105;VDB=0.356839;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,34;MQ=60 GT:PL:AD 1:255,0:0,97 -MN908947.3 14676 . C T 225.417 . DP=105;VDB=0.069958;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,22;MQ=60 GT:PL:AD 1:255,0:0,101 -MN908947.3 15279 . C T 225.417 . DP=86;VDB=0.0709772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,16;MQ=60 GT:PL:AD 1:255,0:0,76 -MN908947.3 16176 . T C 225.417 . DP=66;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,43,14;MQ=60 GT:PL:AD 1:255,0:0,57 -MN908947.3 17615 . A G 225.417 . DP=107;VDB=0.522782;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,42;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 21762 . CTATACA C 228.402 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00293609;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,7,56,12;MQ=60;OLD_CLUMPED=MN908947.3|21762|CTATACAT|CT GT:PL:AD 1:255,0:7,68 -MN908947.3 21764 . ATACATG A 228.421 . INDEL;IDV=73;IMF=0.973333;DP=75;VDB=0.00439388;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,3,56,16;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT GT:PL:AD 1:255,0:3,72 -MN908947.3 21766 . ACATGTC A 228.408 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00444089;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,6,54,13;MQ=60 GT:PL:AD 1:255,0:8,67 -MN908947.3 21990 . TTTA T 228.315 . INDEL;IDV=48;IMF=0.842105;DP=57;VDB=0.851606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,5,32,18;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA GT:PL:AD 1:255,0:7,50 -MN908947.3 23063 . A T 225.417 . DP=27;VDB=0.974241;SGB=-0.692914;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,7,18;MQ=60 GT:PL:AD 1:255,0:0,25 -MN908947.3 23271 . C A 225.417 . DP=113;VDB=0.602922;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,87,25;MQ=60 GT:PL:AD 1:255,0:0,112 -MN908947.3 23403 . A G 225.417 . DP=103;VDB=0.311158;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,74,22;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 23604 . C A 225.417 . DP=103;VDB=0.303274;SGB=-0.693147;MQSB=0.99457;MQ0F=0;AC=1;AN=1;DP4=0,0,71,25;MQ=59 GT:PL:AD 1:255,0:0,96 -MN908947.3 23709 . C T 225.422 . DP=105;VDB=0.072772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,57,46;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 24506 . T G 225.417 . DP=85;VDB=0.0492644;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,15;MQ=60 GT:PL:AD 1:255,0:0,81 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.741848;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,48;MQ=60 GT:PL:AD 1:255,0:0,114 -MN908947.3 25523 . G A 225.417 . DP=117;VDB=0.974641;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,43;MQ=60 GT:PL:AD 1:255,0:0,110 -MN908947.3 25693 . C A 225.417 . DP=50;VDB=0.0160805;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,13;MQ=60 GT:PL:AD 1:255,0:0,44 -MN908947.3 26606 . C T 225.417 . DP=78;VDB=0.00014612;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,15;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 27972 . C T 225.417 . DP=111;VDB=0.913367;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,38;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 28048 . G T 225.417 . DP=89;VDB=0.0584099;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,34;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 28111 . A G 228.412 . DP=77;VDB=0.999359;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,22;MQ=60 GT:PL:AD 1:255,0:1,69 -MN908947.3 28270 . TA T 5.97268 . INDEL;IDV=90;IMF=0.857143;DP=105;VDB=0.23186;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=20,11,53,21;MQ=60;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:115,83:31,74 -MN908947.3 28280 . G C 225.417 . DP=90;VDB=0.00372887;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28281 . A T 225.417 . DP=90;VDB=0.00359238;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28282 . T A 225.417 . DP=91;VDB=0.00367371;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28817 . G T 228.414 . DP=75;VDB=0.460414;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,50,16;MQ=60 GT:PL:AD 1:255,0:1,66 -MN908947.3 28881 . G A 225.417 . DP=78;VDB=0.0391523;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28882 . G A 225.417 . DP=77;VDB=0.0433548;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28883 . G C 225.417 . DP=78;VDB=0.0387719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28977 . C T 225.417 . DP=74;VDB=0.318561;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,37;MQ=60 GT:PL:AD 1:255,0:0,69 diff --git a/benchmark/ERR5401235/ERR5401235.preprocessed.gatk.vcf b/benchmark/ERR5401235/ERR5401235.preprocessed.gatk.vcf deleted file mode 100644 index 14232e7..0000000 --- a/benchmark/ERR5401235/ERR5401235.preprocessed.gatk.vcf +++ /dev/null @@ -1,69 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 25769.04 . AC=1;AF=1.00;AN=1;DP=830;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.62;SOR=0.731 GT:AD:DP:GQ:PL 1:0,815:815:99:25779,0 -MN908947.3 913 . C T 40839.04 . AC=1;AF=1.00;AN=1;DP=1291;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.80;SOR=1.744 GT:AD:DP:GQ:PL 1:0,1245:1245:99:40849,0 -MN908947.3 1968 . C T 6696.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.221;DP=204;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.99;ReadPosRankSum=-1.385;SOR=0.554 GT:AD:DP:GQ:PL 1:1,202:203:99:6706,0 -MN908947.3 2761 . A G 13866.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.303;DP=434;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.66;ReadPosRankSum=-0.269;SOR=0.627 GT:AD:DP:GQ:PL 1:1,411:412:99:13876,0 -MN908947.3 3037 . C T 37041.04 . AC=1;AF=1.00;AN=1;DP=1208;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.34;SOR=1.359 GT:AD:DP:GQ:PL 1:0,1182:1182:99:38023,0 -MN908947.3 3267 . C T 50181.04 . AC=1;AF=1.00;AN=1;DP=1475;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.42;SOR=2.149 GT:AD:DP:GQ:PL 1:0,1458:1458:99:50191,0 -MN908947.3 5388 . C A 31466.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.785;DP=921;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.69;ReadPosRankSum=1.679;SOR=1.242 GT:AD:DP:GQ:PL 1:1,906:907:99:31476,0 -MN908947.3 5986 . C T 21910.04 . AC=1;AF=1.00;AN=1;DP=694;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.71;SOR=2.566 GT:AD:DP:GQ:PL 1:0,691:691:99:24847,0 -MN908947.3 6954 . T C 13303.04 . AC=1;AF=1.00;AN=1;DP=405;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.11;SOR=2.114 GT:AD:DP:GQ:PL 1:0,390:390:99:13313,0 -MN908947.3 7675 . G T 17267.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.999;DP=476;FS=15.675;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.28;ReadPosRankSum=1.178;SOR=3.293 GT:AD:DP:GQ:PL 1:8,467:475:99:17277,0 -MN908947.3 10329 . A G 58466.04 . AC=1;AF=1.00;AN=1;DP=1773;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.07;SOR=1.975 GT:AD:DP:GQ:PL 1:0,1768:1768:99:58476,0 -MN908947.3 11287 . GTCTGGTTTT G 55813.04 . AC=1;AF=1.00;AN=1;DP=1674;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.95;SOR=2.292 GT:AD:DP:GQ:PL 1:0,1597:1597:99:71155,0 -MN908947.3 11379 . C T 4277.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=7.491;DP=749;FS=162.273;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=5.94;ReadPosRankSum=14.031;SOR=3.426 GT:AD:DP:GQ:PL 1:317,403:720:99:4287,0 -MN908947.3 12162 . A G 43054.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.848;DP=1287;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.05;ReadPosRankSum=-1.150;SOR=0.240 GT:AD:DP:GQ:PL 1:1,1211:1212:99:43064,0 -MN908947.3 14408 . C T 35969.04 . AC=1;AF=1.00;AN=1;DP=1119;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.12;SOR=0.834 GT:AD:DP:GQ:PL 1:0,1086:1086:99:35979,0 -MN908947.3 14676 . C T 47309.04 . AC=1;AF=1.00;AN=1;DP=1388;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.02;QD=34.71;SOR=1.938 GT:AD:DP:GQ:PL 1:0,1363:1363:99:47319,0 -MN908947.3 15279 . C T 26872.04 . AC=1;AF=1.00;AN=1;DP=807;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.89;SOR=2.361 GT:AD:DP:GQ:PL 1:0,793:793:99:26882,0 -MN908947.3 16176 . T C 24767.04 . AC=1;AF=1.00;AN=1;DP=769;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.79;SOR=0.909 GT:AD:DP:GQ:PL 1:0,712:712:99:24777,0 -MN908947.3 17615 . A G 38275.04 . AC=1;AF=1.00;AN=1;DP=1208;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.44;SOR=1.728 GT:AD:DP:GQ:PL 1:0,1180:1180:99:38285,0 -MN908947.3 21764 . ATACATG A 32015.01 . AC=1;AF=1.00;AN=1;DP=770;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.78;SOR=1.800 GT:AD:DP:GQ:PL 1:0,719:719:99:32025,0 -MN908947.3 21990 . TTTA T 17155.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.129;DP=510;FS=2.597;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.71;ReadPosRankSum=2.176;SOR=0.265 GT:AD:DP:GQ:PL 1:7,480:487:99:17165,0 -MN908947.3 23063 . A T 1381.04 . AC=1;AF=1.00;AN=1;DP=39;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=25.98;SOR=1.923 GT:AD:DP:GQ:PL 1:0,39:39:99:1391,0 -MN908947.3 23271 . C A 47873.04 . AC=1;AF=1.00;AN=1;DP=1497;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.68;SOR=1.886 GT:AD:DP:GQ:PL 1:0,1465:1465:99:47883,0 -MN908947.3 23403 . A G 48501.04 . AC=1;AF=1.00;AN=1;DP=1496;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.95;SOR=1.465 GT:AD:DP:GQ:PL 1:0,1472:1472:99:48511,0 -MN908947.3 23604 . C A 35101.04 . AC=1;AF=1.00;AN=1;DP=1037;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.35;SOR=1.036 GT:AD:DP:GQ:PL 1:0,1022:1022:99:35111,0 -MN908947.3 23709 . C T 42135.04 . AC=1;AF=1.00;AN=1;DP=1292;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.89;SOR=2.400 GT:AD:DP:GQ:PL 1:0,1281:1281:99:42145,0 -MN908947.3 24506 . T G 27484.04 . AC=1;AF=1.00;AN=1;DP=760;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.76;SOR=2.839 GT:AD:DP:GQ:PL 1:0,750:750:99:27494,0 -MN908947.3 24914 . G C 64796.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.056;DP=2004;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.21;ReadPosRankSum=-0.539;SOR=1.023 GT:AD:DP:GQ:PL 1:1,1950:1951:99:64806,0 -MN908947.3 25523 . G A 43422.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.287;DP=1307;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.77;ReadPosRankSum=1.894;SOR=1.971 GT:AD:DP:GQ:PL 1:2,1284:1286:99:43432,0 -MN908947.3 25693 . C A 6380.04 . AC=1;AF=1.00;AN=1;DP=174;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.69;SOR=3.016 GT:AD:DP:GQ:PL 1:0,171:171:99:6390,0 -MN908947.3 26606 . C T 43051.04 . AC=1;AF=1.00;AN=1;DP=1153;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.32;SOR=2.946 GT:AD:DP:GQ:PL 1:0,1140:1140:99:43061,0 -MN908947.3 27972 . C T 33207.04 . AC=1;AF=1.00;AN=1;DP=1059;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.15;SOR=0.844 GT:AD:DP:GQ:PL 1:0,1033:1033:99:33217,0 -MN908947.3 28048 . G T 29092.04 . AC=1;AF=1.00;AN=1;DP=893;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.76;SOR=1.723 GT:AD:DP:GQ:PL 1:0,888:888:99:29102,0 -MN908947.3 28111 . A G 30582.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.136;DP=927;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.56;ReadPosRankSum=0.167;SOR=0.288 GT:AD:DP:GQ:PL 1:1,884:885:99:30592,0 -MN908947.3 28270 . TA T 55890.01 . AC=1;AF=1.00;AN=1;DP=1323;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=35.24;SOR=0.736 GT:AD:DP:GQ:PL 1:0,1271:1271:99:55900,0 -MN908947.3 28280 . G C 53412.04 . AC=1;AF=1.00;AN=1;DP=1201;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.02;SOR=0.923 GT:AD:DP:GQ:PL 1:0,1201:1201:99:53422,0 -MN908947.3 28281 . A T 53355.04 . AC=1;AF=1.00;AN=1;DP=1209;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.37;SOR=0.920 GT:AD:DP:GQ:PL 1:0,1199:1199:99:53365,0 -MN908947.3 28282 . T A 53356.04 . AC=1;AF=1.00;AN=1;DP=1220;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.98;SOR=0.920 GT:AD:DP:GQ:PL 1:0,1199:1199:99:53366,0 -MN908947.3 28817 . G T 13353.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.794;DP=400;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.15;ReadPosRankSum=-0.758;SOR=1.236 GT:AD:DP:GQ:PL 1:1,390:391:99:13363,0 -MN908947.3 28881 . G A 14820.04 . AC=1;AF=1.00;AN=1;DP=338;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.58;SOR=1.242 GT:AD:DP:GQ:PL 1:0,332:332:99:14830,0 -MN908947.3 28882 . G A 14820.04 . AC=1;AF=1.00;AN=1;DP=340;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.70;SOR=1.242 GT:AD:DP:GQ:PL 1:0,332:332:99:14830,0 -MN908947.3 28883 . G C 14820.04 . AC=1;AF=1.00;AN=1;DP=353;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.75;SOR=1.242 GT:AD:DP:GQ:PL 1:0,332:332:99:14830,0 -MN908947.3 28977 . C T 9796.04 . AC=1;AF=1.00;AN=1;DP=272;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.32;SOR=2.950 GT:AD:DP:GQ:PL 1:0,266:266:99:9806,0 diff --git a/benchmark/ERR5401235/ERR5401235.preprocessed.ivar.tsv b/benchmark/ERR5401235/ERR5401235.preprocessed.ivar.tsv deleted file mode 100644 index e4a62d7..0000000 --- a/benchmark/ERR5401235/ERR5401235.preprocessed.ivar.tsv +++ /dev/null @@ -1,93 +0,0 @@ -REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA -MN908947.3 241 C T 0 0 0 588 180 51 1 588 0 TRUE NA NA NA NA NA -MN908947.3 913 C T 0 0 0 978 542 53 1 978 0 TRUE CDS:ENSSASP00005000003 TCC S TCT S -MN908947.3 913 C T 0 0 0 978 542 53 1 978 0 TRUE CDS:ENSSASP00005000002 TCC S TCT S -MN908947.3 1946 G -N 198 65 45 8 0 20 0.0314961 254 0.0256182 FALSE NA NA NA NA NA -MN908947.3 1968 C T 1 0 39 154 23 49 0.993548 155 2.46736e-105 TRUE CDS:ENSSASP00005000003 ACA T ATA I -MN908947.3 1968 C T 1 0 39 154 23 49 0.993548 155 2.46736e-105 TRUE CDS:ENSSASP00005000002 ACA T ATA I -MN908947.3 2761 A G 1 1 39 326 174 49 0.996942 327 8.28944e-224 TRUE CDS:ENSSASP00005000003 GAA E GAG E -MN908947.3 2761 A G 1 1 39 326 174 49 0.996942 327 8.28944e-224 TRUE CDS:ENSSASP00005000002 GAA E GAG E -MN908947.3 3037 C T 0 0 0 852 417 52 1 852 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 3037 C T 0 0 0 852 417 52 1 852 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 3267 C T 0 0 0 1161 31 49 1 1161 0 TRUE CDS:ENSSASP00005000003 ACT T ATT I -MN908947.3 3267 C T 0 0 0 1161 31 49 1 1161 0 TRUE CDS:ENSSASP00005000002 ACT T ATT I -MN908947.3 4080 G T 350 141 44 12 0 36 0.0331492 362 6.3643e-05 TRUE CDS:ENSSASP00005000003 AGT S ATT I -MN908947.3 4080 G T 350 141 44 12 0 36 0.0331492 362 6.3643e-05 TRUE CDS:ENSSASP00005000002 AGT S ATT I -MN908947.3 5388 C A 0 0 0 734 19 48 1 734 0 TRUE CDS:ENSSASP00005000003 GCT A GAT D -MN908947.3 5388 C A 0 0 0 734 19 48 1 734 0 TRUE CDS:ENSSASP00005000002 GCT A GAT D -MN908947.3 5986 C T 0 0 0 601 28 47 1 601 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 5986 C T 0 0 0 601 28 47 1 601 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 6954 T C 0 0 0 298 192 49 1 298 2.22436e-204 TRUE CDS:ENSSASP00005000003 ATA I ACA T -MN908947.3 6954 T C 0 0 0 298 192 49 1 298 2.22436e-204 TRUE CDS:ENSSASP00005000002 ATA I ACA T -MN908947.3 7398 C T 32 16 42 1 1 31 0.030303 33 0.464789 FALSE CDS:ENSSASP00005000003 TCA S TTA L -MN908947.3 7398 C T 32 16 42 1 1 31 0.030303 33 0.464789 FALSE CDS:ENSSASP00005000002 TCA S TTA L -MN908947.3 7519 A T 24 11 52 1 0 78 0.04 25 0.416667 FALSE CDS:ENSSASP00005000003 GCA A GCT A -MN908947.3 7519 A T 24 11 52 1 0 78 0.04 25 0.416667 FALSE CDS:ENSSASP00005000002 GCA A GCT A -MN908947.3 7602 A T 26 18 47 2 1 55 0.0714286 28 0.199894 FALSE CDS:ENSSASP00005000003 AAA K ATA I -MN908947.3 7602 A T 26 18 47 2 1 55 0.0714286 28 0.199894 FALSE CDS:ENSSASP00005000002 AAA K ATA I -MN908947.3 7667 G C 382 9 43 12 0 40 0.0304569 394 8.72984e-05 TRUE CDS:ENSSASP00005000003 GAA E CAA Q -MN908947.3 7667 G C 382 9 43 12 0 40 0.0304569 394 8.72984e-05 TRUE CDS:ENSSASP00005000002 GAA E CAA Q -MN908947.3 7675 G T 7 4 47 446 3 44 0.984547 453 3.58247e-280 TRUE CDS:ENSSASP00005000003 GCG A GCT A -MN908947.3 7675 G T 7 4 47 446 3 44 0.984547 453 3.58247e-280 TRUE CDS:ENSSASP00005000002 GCG A GCT A -MN908947.3 7728 C T 679 3 48 92 1 49 0.119326 771 2.41861e-35 TRUE CDS:ENSSASP00005000003 TCT S TTT F -MN908947.3 7728 C T 679 3 48 92 1 49 0.119326 771 2.41861e-35 TRUE CDS:ENSSASP00005000002 TCT S TTT F -MN908947.3 10329 A G 0 0 0 1361 846 51 1 1361 0 TRUE CDS:ENSSASP00005000003 GAT D GGT G -MN908947.3 10329 A G 0 0 0 1361 846 51 1 1361 0 TRUE CDS:ENSSASP00005000002 GAT D GGT G -MN908947.3 10986 G T 183 159 41 7 5 45 0.0368421 190 0.00447269 TRUE CDS:ENSSASP00005000003 AGA R ATA I -MN908947.3 10986 G T 183 159 41 7 5 45 0.0368421 190 0.00447269 TRUE CDS:ENSSASP00005000002 AGA R ATA I -MN908947.3 11074 C -N 1236 8 45 53 0 20 0.0345052 1536 3.83783e-08 TRUE NA NA NA NA NA -MN908947.3 11074 C +T 1236 8 45 61 0 20 0.0397135 1536 4.5394e-10 TRUE NA NA NA NA NA -MN908947.3 11287 G -NNNNNNNNN 1355 927 49 1642 0 20 0.921954 1781 0 TRUE NA NA NA NA NA -MN908947.3 11288 T A 0 0 0 18 4 36 1 18 1.19833e-41 TRUE CDS:ENSSASP00005000003 TCT S ACT T -MN908947.3 11288 T A 0 0 0 18 4 36 1 18 1.19833e-41 TRUE CDS:ENSSASP00005000002 TCT S ACT T -MN908947.3 11291 G A 0 0 0 9 1 32 1 9 3.87458e-23 TRUE CDS:ENSSASP00005000003 GGT G AGT S -MN908947.3 11291 G A 0 0 0 9 1 32 1 9 3.87458e-23 TRUE CDS:ENSSASP00005000002 GGT G AGT S -MN908947.3 11296 T G 0 0 0 10 1 66 1 10 2.20965e-26 TRUE CDS:ENSSASP00005000003 TTT F TTG L -MN908947.3 11296 T G 0 0 0 10 1 66 1 10 2.20965e-26 TRUE CDS:ENSSASP00005000002 TTT F TTG L -MN908947.3 11379 C T 320 226 44 370 11 41 0.536232 690 2.64454e-160 TRUE CDS:ENSSASP00005000003 GCT A GTT V -MN908947.3 11379 C T 320 226 44 370 11 41 0.536232 690 2.64454e-160 TRUE CDS:ENSSASP00005000002 GCT A GTT V -MN908947.3 12162 A G 1 1 39 1015 422 43 0.999016 1016 0 TRUE CDS:ENSSASP00005000003 CAG Q CGG R -MN908947.3 12162 A G 1 1 39 1015 422 43 0.999016 1016 0 TRUE CDS:ENSSASP00005000002 CAG Q CGG R -MN908947.3 13390 G T 126 37 49 7 1 57 0.0526316 133 0.0023848 TRUE CDS:ENSSASP00005000003 ATG M ATT I -MN908947.3 13390 G T 126 37 49 7 1 57 0.0526316 133 0.0023848 TRUE CDS:ENSSASP00005000002 ATG M ATT I -MN908947.3 14408 C T 0 0 0 812 227 51 1 812 0 TRUE CDS:ENSSASP00005000002 CTA L TTA L -MN908947.3 14676 C T 0 0 0 1135 54 50 1 1135 0 TRUE CDS:ENSSASP00005000002 CCG P CTG L -MN908947.3 15279 C T 0 0 0 608 3 49 1 608 0 TRUE CDS:ENSSASP00005000002 ACC T ATC I -MN908947.3 16176 T C 0 0 0 603 280 45 1 603 0 TRUE CDS:ENSSASP00005000002 CTT L CCT P -MN908947.3 17615 A G 0 0 0 885 504 53 1 885 0 TRUE CDS:ENSSASP00005000002 AGC S GGC G -MN908947.3 17738 C T 396 223 44 21 18 38 0.0503597 417 3.39964e-08 TRUE CDS:ENSSASP00005000002 CAC H TAC Y -MN908947.3 21667 T G 270 124 48 21 0 35 0.0721649 291 9.23112e-09 TRUE CDS:ENSSASP00005000004 GGT G GGG G -MN908947.3 21764 A -NNNNNN 600 7 51 800 0 20 0.968523 826 7.75074e-200 TRUE NA NA NA NA NA -MN908947.3 21766 A C 0 0 0 1 1 33 1 1 0.00124378 TRUE CDS:ENSSASP00005000004 ATA I ATC I -MN908947.3 21770 G A 0 0 0 19 11 43 1 19 3.74308e-39 TRUE CDS:ENSSASP00005000004 GTC V ATC I -MN908947.3 21990 T -NNN 411 240 43 410 0 20 0.835031 491 3.23545e-99 TRUE NA NA NA NA NA -MN908947.3 22520 G C 41 24 51 2 1 58 0.0465116 43 0.178812 FALSE CDS:ENSSASP00005000004 GTC V CTC L -MN908947.3 22858 C T 401 303 42 16 10 45 0.0383693 417 2.61078e-06 TRUE CDS:ENSSASP00005000004 TGC C TGT C -MN908947.3 22998 C T 26 4 58 1 0 78 0.037037 27 0.391304 FALSE CDS:ENSSASP00005000004 CCT P CTT L -MN908947.3 23063 A T 0 0 0 33 22 45 1 33 2.89251e-21 TRUE CDS:ENSSASP00005000004 AAT N TAT Y -MN908947.3 23099 C T 24 18 40 1 1 33 0.04 25 0.490196 FALSE CDS:ENSSASP00005000004 CTT L TTT F -MN908947.3 23147 A +G 332 14 43 13 0 20 0.0321782 404 0.0103316 FALSE NA NA NA NA NA -MN908947.3 23271 C A 0 0 0 1113 5 53 1 1113 0 TRUE CDS:ENSSASP00005000004 GCT A GAT D -MN908947.3 23403 A G 0 0 0 1196 639 52 1 1196 0 TRUE CDS:ENSSASP00005000004 GAT D GGT G -MN908947.3 23604 C A 1 0 20 987 113 50 0.998988 988 0 TRUE CDS:ENSSASP00005000004 CCT P CAT H -MN908947.3 23608 G T 914 136 48 33 6 51 0.0348469 947 2.6481e-13 TRUE CDS:ENSSASP00005000004 CGG R CGT R -MN908947.3 23709 C T 0 0 0 1020 640 50 1 1020 0 TRUE CDS:ENSSASP00005000004 ACA T ATA I -MN908947.3 24506 T G 0 0 0 695 7 46 1 695 0 TRUE CDS:ENSSASP00005000004 TCA S GCA A -MN908947.3 24914 G C 1 1 32 1524 969 48 0.999344 1525 0 TRUE CDS:ENSSASP00005000004 GAC D CAC H -MN908947.3 25523 G A 1 0 62 1025 649 50 0.999025 1026 0 TRUE CDS:ENSSASP00005000006 GGA G GAA E -MN908947.3 25693 C A 0 0 0 153 17 42 1 153 1.14828e-99 TRUE CDS:ENSSASP00005000006 CTT L ATT I -MN908947.3 26606 C T 0 0 0 1146 11 45 1 1146 0 TRUE CDS:ENSSASP00005000007 TTC F TTT F -MN908947.3 27578 A G 30 2 48 1 0 77 0.0322581 31 0.43662 FALSE CDS:ENSSASP00005000009 CAA Q CGA R -MN908947.3 27603 C T 29 2 51 1 0 75 0.0333333 30 0.410959 FALSE CDS:ENSSASP00005000009 GGC G GGT G -MN908947.3 27972 C T 0 0 0 730 230 55 1 730 0 TRUE CDS:ENSSASP00005000008 CAA Q TAA * -MN908947.3 28048 G T 0 0 0 649 357 53 1 649 0 TRUE CDS:ENSSASP00005000008 AGA R ATA I -MN908947.3 28111 A G 1 0 38 797 237 45 0.998747 798 0 TRUE CDS:ENSSASP00005000008 TAC Y TGC C -MN908947.3 28270 T -N 1017 253 52 1205 0 20 0.843838 1428 1.58902e-311 TRUE NA NA NA NA NA -MN908947.3 28280 G C 0 0 0 860 325 49 1 860 0 TRUE CDS:ENSSASP00005000005 GAT D CAT H -MN908947.3 28281 A T 0 0 0 858 327 49 0.998836 859 0 TRUE CDS:ENSSASP00005000005 GAT D GTT V -MN908947.3 28282 T A 0 0 0 880 344 50 0.998865 881 0 TRUE CDS:ENSSASP00005000005 GAT D GAA E -MN908947.3 28817 G T 0 0 0 313 8 47 1 313 9.4904e-215 TRUE CDS:ENSSASP00005000005 GCC A TCC S -MN908947.3 28881 G A 0 0 0 241 106 47 1 241 1.81192e-165 TRUE CDS:ENSSASP00005000005 AGG R AAG K -MN908947.3 28882 G A 0 0 0 244 105 46 1 244 2.585e-166 TRUE CDS:ENSSASP00005000005 AGG R AGA R -MN908947.3 28883 G C 0 0 0 248 110 47 1 248 3.04198e-169 TRUE CDS:ENSSASP00005000005 GGA G CGA R -MN908947.3 28977 C T 0 0 0 244 182 43 1 244 8.51086e-163 TRUE CDS:ENSSASP00005000005 TCT S TTT F diff --git a/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter01.vcf b/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter01.vcf deleted file mode 100644 index cbd0428..0000000 --- a/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter01.vcf +++ /dev/null @@ -1,63 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5401235/ERR5401235.preprocessed.lofreq.vcf ERR5401235/ERR5401235.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.1' ./ERR5401235/ERR5401235.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:26 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 29131 PASS DP=836;AF=0.97488;SB=0;DP4=0,0,412,424 -MN908947.3 913 . C T 49314 PASS DP=1416;AF=0.96822;SB=0;DP4=0,0,438,976 -MN908947.3 1968 . C T 7499 PASS DP=211;AF=0.938389;SB=0;DP4=1,0,135,75 -MN908947.3 2761 . A G 15584 PASS DP=439;AF=0.961276;SB=0;DP4=0,1,156,282 -MN908947.3 3037 . C T 43045 PASS DP=1208;AF=0.965232;SB=0;DP4=0,0,434,772 -MN908947.3 3267 . C T 49314 PASS DP=1540;AF=0.979221;SB=0;DP4=0,0,1143,397 -MN908947.3 5388 . C A 35297 PASS DP=968;AF=0.96281;SB=0;DP4=1,0,738,225 -MN908947.3 5986 . C T 27517 PASS DP=754;AF=0.976127;SB=0;DP4=0,0,579,167 -MN908947.3 6954 . T C 14394 PASS DP=391;AF=0.97954;SB=0;DP4=0,0,105,286 -MN908947.3 7675 . G T 19119 PASS DP=535;AF=0.973832;SB=35;DP4=2,6,447,80 -MN908947.3 7728 . C T 2912 PASS DP=998;AF=0.119238;SB=1;DP4=691,187,92,28 -MN908947.3 10329 . A G 49314 PASS DP=1883;AF=0.967074;SB=0;DP4=0,0,517,1365 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=1661;AF=0.988561;SB=13;DP4=43,94,387,1255;INDEL;HRUN=1 -MN908947.3 12162 . A G 43713 PASS DP=1260;AF=0.950794;SB=3;DP4=0,2,613,642 -MN908947.3 14408 . C T 40848 PASS DP=1115;AF=0.974888;SB=0;DP4=0,0,592,523 -MN908947.3 14676 . C T 49314 PASS DP=1525;AF=0.979672;SB=0;DP4=0,0,1090,435 -MN908947.3 15279 . C T 29261 PASS DP=816;AF=0.979167;SB=0;DP4=0,0,617,199 -MN908947.3 16176 . T C 26661 PASS DP=754;AF=0.965517;SB=0;DP4=0,0,331,423 -MN908947.3 17615 . A G 45626 PASS DP=1253;AF=0.971269;SB=0;DP4=0,0,378,873 -MN908947.3 21764 . ATACATG A 29457 PASS DP=826;AF=0.968523;SB=44;DP4=9,17,593,207;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 15359 PASS DP=490;AF=0.834694;SB=24;DP4=17,64,155,254;INDEL;HRUN=3 -MN908947.3 23063 . A T 1458 PASS DP=40;AF=0.975;SB=0;DP4=0,0,11,29 -MN908947.3 23271 . C A 49314 PASS DP=1624;AF=0.964286;SB=0;DP4=1,0,1147,476 -MN908947.3 23403 . A G 49314 PASS DP=1702;AF=0.96416;SB=0;DP4=0,1,560,1141 -MN908947.3 23604 . C A 48431 PASS DP=1344;AF=0.970238;SB=0;DP4=1,1,886,454 -MN908947.3 23709 . C T 49314 PASS DP=1410;AF=0.919858;SB=5;DP4=1,0,382,1023 -MN908947.3 24506 . T G 31517 PASS DP=872;AF=0.961009;SB=0;DP4=1,0,709,159 -MN908947.3 24914 . G C 49314 PASS DP=2052;AF=0.975634;SB=0;DP4=0,1,560,1490 -MN908947.3 25523 . G A 49314 PASS DP=1396;AF=0.974212;SB=0;DP4=1,2,381,1012 -MN908947.3 25693 . C A 6293 PASS DP=182;AF=0.93956;SB=0;DP4=0,0,146,36 -MN908947.3 26606 . C T 49314 PASS DP=1375;AF=0.985455;SB=0;DP4=0,0,1135,240 -MN908947.3 27972 . C T 39658 PASS DP=1079;AF=0.974977;SB=0;DP4=0,0,506,573 -MN908947.3 28048 . G T 34665 PASS DP=934;AF=0.972163;SB=0;DP4=0,0,293,634 -MN908947.3 28111 . A G 34812 PASS DP=1015;AF=0.960591;SB=0;DP4=2,1,570,442 -MN908947.3 28270 . TA T 26983 PASS DP=1427;AF=0.843728;SB=69;DP4=157,66,618,586;INDEL;HRUN=4 -MN908947.3 28280 . G C 24538 PASS DP=1128;AF=0.970745;SB=0;DP4=0,0,542,585 -MN908947.3 28281 . A T 24631 PASS DP=1128;AF=0.971631;SB=3;DP4=1,0,540,586 -MN908947.3 28282 . T A 25254 PASS DP=1167;AF=0.976864;SB=0;DP4=0,0,546,618 -MN908947.3 28817 . G T 14471 PASS DP=413;AF=0.934625;SB=0;DP4=2,0,312,99 -MN908947.3 28881 . G A 11321 PASS DP=320;AF=0.93125;SB=0;DP4=0,0,143,177 -MN908947.3 28882 . G A 11209 PASS DP=319;AF=0.952978;SB=0;DP4=0,0,142,177 -MN908947.3 28883 . G C 11646 PASS DP=325;AF=0.966154;SB=0;DP4=0,0,142,183 -MN908947.3 28977 . C T 10463 PASS DP=304;AF=0.917763;SB=6;DP4=1,0,66,237 diff --git a/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter02.vcf b/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter02.vcf deleted file mode 100644 index bb11ebd..0000000 --- a/benchmark/ERR5401235/ERR5401235.preprocessed.lofreq.vcf.filter02.vcf +++ /dev/null @@ -1,62 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5401235/ERR5401235.preprocessed.lofreq.vcf ERR5401235/ERR5401235.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' ./ERR5401235/ERR5401235.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:26 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 29131 PASS DP=836;AF=0.97488;SB=0;DP4=0,0,412,424 -MN908947.3 913 . C T 49314 PASS DP=1416;AF=0.96822;SB=0;DP4=0,0,438,976 -MN908947.3 1968 . C T 7499 PASS DP=211;AF=0.938389;SB=0;DP4=1,0,135,75 -MN908947.3 2761 . A G 15584 PASS DP=439;AF=0.961276;SB=0;DP4=0,1,156,282 -MN908947.3 3037 . C T 43045 PASS DP=1208;AF=0.965232;SB=0;DP4=0,0,434,772 -MN908947.3 3267 . C T 49314 PASS DP=1540;AF=0.979221;SB=0;DP4=0,0,1143,397 -MN908947.3 5388 . C A 35297 PASS DP=968;AF=0.96281;SB=0;DP4=1,0,738,225 -MN908947.3 5986 . C T 27517 PASS DP=754;AF=0.976127;SB=0;DP4=0,0,579,167 -MN908947.3 6954 . T C 14394 PASS DP=391;AF=0.97954;SB=0;DP4=0,0,105,286 -MN908947.3 7675 . G T 19119 PASS DP=535;AF=0.973832;SB=35;DP4=2,6,447,80 -MN908947.3 10329 . A G 49314 PASS DP=1883;AF=0.967074;SB=0;DP4=0,0,517,1365 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=1661;AF=0.988561;SB=13;DP4=43,94,387,1255;INDEL;HRUN=1 -MN908947.3 12162 . A G 43713 PASS DP=1260;AF=0.950794;SB=3;DP4=0,2,613,642 -MN908947.3 14408 . C T 40848 PASS DP=1115;AF=0.974888;SB=0;DP4=0,0,592,523 -MN908947.3 14676 . C T 49314 PASS DP=1525;AF=0.979672;SB=0;DP4=0,0,1090,435 -MN908947.3 15279 . C T 29261 PASS DP=816;AF=0.979167;SB=0;DP4=0,0,617,199 -MN908947.3 16176 . T C 26661 PASS DP=754;AF=0.965517;SB=0;DP4=0,0,331,423 -MN908947.3 17615 . A G 45626 PASS DP=1253;AF=0.971269;SB=0;DP4=0,0,378,873 -MN908947.3 21764 . ATACATG A 29457 PASS DP=826;AF=0.968523;SB=44;DP4=9,17,593,207;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 15359 PASS DP=490;AF=0.834694;SB=24;DP4=17,64,155,254;INDEL;HRUN=3 -MN908947.3 23063 . A T 1458 PASS DP=40;AF=0.975;SB=0;DP4=0,0,11,29 -MN908947.3 23271 . C A 49314 PASS DP=1624;AF=0.964286;SB=0;DP4=1,0,1147,476 -MN908947.3 23403 . A G 49314 PASS DP=1702;AF=0.96416;SB=0;DP4=0,1,560,1141 -MN908947.3 23604 . C A 48431 PASS DP=1344;AF=0.970238;SB=0;DP4=1,1,886,454 -MN908947.3 23709 . C T 49314 PASS DP=1410;AF=0.919858;SB=5;DP4=1,0,382,1023 -MN908947.3 24506 . T G 31517 PASS DP=872;AF=0.961009;SB=0;DP4=1,0,709,159 -MN908947.3 24914 . G C 49314 PASS DP=2052;AF=0.975634;SB=0;DP4=0,1,560,1490 -MN908947.3 25523 . G A 49314 PASS DP=1396;AF=0.974212;SB=0;DP4=1,2,381,1012 -MN908947.3 25693 . C A 6293 PASS DP=182;AF=0.93956;SB=0;DP4=0,0,146,36 -MN908947.3 26606 . C T 49314 PASS DP=1375;AF=0.985455;SB=0;DP4=0,0,1135,240 -MN908947.3 27972 . C T 39658 PASS DP=1079;AF=0.974977;SB=0;DP4=0,0,506,573 -MN908947.3 28048 . G T 34665 PASS DP=934;AF=0.972163;SB=0;DP4=0,0,293,634 -MN908947.3 28111 . A G 34812 PASS DP=1015;AF=0.960591;SB=0;DP4=2,1,570,442 -MN908947.3 28270 . TA T 26983 PASS DP=1427;AF=0.843728;SB=69;DP4=157,66,618,586;INDEL;HRUN=4 -MN908947.3 28280 . G C 24538 PASS DP=1128;AF=0.970745;SB=0;DP4=0,0,542,585 -MN908947.3 28281 . A T 24631 PASS DP=1128;AF=0.971631;SB=3;DP4=1,0,540,586 -MN908947.3 28282 . T A 25254 PASS DP=1167;AF=0.976864;SB=0;DP4=0,0,546,618 -MN908947.3 28817 . G T 14471 PASS DP=413;AF=0.934625;SB=0;DP4=2,0,312,99 -MN908947.3 28881 . G A 11321 PASS DP=320;AF=0.93125;SB=0;DP4=0,0,143,177 -MN908947.3 28882 . G A 11209 PASS DP=319;AF=0.952978;SB=0;DP4=0,0,142,177 -MN908947.3 28883 . G C 11646 PASS DP=325;AF=0.966154;SB=0;DP4=0,0,142,183 -MN908947.3 28977 . C T 10463 PASS DP=304;AF=0.917763;SB=6;DP4=1,0,66,237 diff --git a/benchmark/ERR5401235/ERR5401235.vcf b/benchmark/ERR5401235/ERR5401235.vcf deleted file mode 100644 index 04c6e52..0000000 --- a/benchmark/ERR5401235/ERR5401235.vcf +++ /dev/null @@ -1,73 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5401235/ERR5401235.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5401235.vcf; Date=Mon Jun 7 15:54:45 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=109;VDB=0.73659;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,37;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 913 . C T 225.417 . DP=102;VDB=0.059221;SGB=-0.693147;MQSB=0.992652;MQ0F=0;AC=1;AN=1;DP4=0,0,65,31;MQ=59 GT:PL:AD 1:255,0:0,96 -MN908947.3 1968 . C T 225.417 . DP=57;VDB=0.18868;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,35,14;MQ=60 GT:PL:AD 1:255,0:0,49 -MN908947.3 2761 . A G 225.417 . DP=84;VDB=0.524286;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,41;MQ=60 GT:PL:AD 1:255,0:0,77 -MN908947.3 3037 . C T 225.417 . DP=94;VDB=0.666921;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,35;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 3267 . C T 225.417 . DP=105;VDB=0.185938;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,81,17;MQ=60 GT:PL:AD 1:255,0:0,98 -MN908947.3 5388 . C A 225.417 . DP=88;VDB=0.109619;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,22;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 5986 . C T 225.417 . DP=84;VDB=0.159577;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,18;MQ=60 GT:PL:AD 1:255,0:0,77 -MN908947.3 6954 . T C 225.417 . DP=85;VDB=0.519512;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,40,38;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 7675 . G T 175.17 . DP=51;VDB=9.90477e-09;SGB=-0.693146;RPB=0.0094;MQB=1;MQSB=1;BQB=0.767974;MQ0F=0;AC=1;AN=1;DP4=3,2,39,5;MQ=60 GT:PL:AD 1:244,42:5,44 -MN908947.3 10329 . A G 225.417 . DP=114;VDB=0.37684;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,43;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 11287 . GTCTGGTTTT G 228.365 . INDEL;IDV=96;IMF=0.941176;DP=102;VDB=0.00658878;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=5,7,61,29;MQ=60 GT:PL:AD 1:255,0:12,90 -MN908947.3 11296 . T G 36.4154 . DP=5;VDB=0.036923;SGB=-0.511536;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,2,1;MQ=60 GT:PL:AD 1:66,0:0,3 -MN908947.3 12162 . A G 225.417 . DP=113;VDB=0.533476;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,75,30;MQ=60 GT:PL:AD 1:255,0:0,105 -MN908947.3 14408 . C T 225.417 . DP=105;VDB=0.356839;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,63,34;MQ=60 GT:PL:AD 1:255,0:0,97 -MN908947.3 14676 . C T 225.417 . DP=105;VDB=0.069958;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,22;MQ=60 GT:PL:AD 1:255,0:0,101 -MN908947.3 15279 . C T 225.417 . DP=86;VDB=0.0709772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,60,16;MQ=60 GT:PL:AD 1:255,0:0,76 -MN908947.3 16176 . T C 225.417 . DP=66;VDB=1;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,43,14;MQ=60 GT:PL:AD 1:255,0:0,57 -MN908947.3 17615 . A G 225.417 . DP=107;VDB=0.522782;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,58,42;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 21762 . CTATACAT CT 228.402 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00293609;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,7,56,12;MQ=60 GT:PL:AD 1:255,0:7,68 -MN908947.3 21764 . ATACATGT AT 228.421 . INDEL;IDV=73;IMF=0.973333;DP=75;VDB=0.00439388;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,3,56,16;MQ=60 GT:PL:AD 1:255,0:3,72 -MN908947.3 21766 . ACATGTC A 228.408 . INDEL;IDV=1;IMF=0.0133333;DP=75;VDB=0.00444089;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,6,54,13;MQ=60 GT:PL:AD 1:255,0:8,67 -MN908947.3 21990 . TTTATTA TTTA 228.315 . INDEL;IDV=48;IMF=0.842105;DP=57;VDB=0.851606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,5,32,18;MQ=60 GT:PL:AD 1:255,0:7,50 -MN908947.3 23063 . A T 225.417 . DP=27;VDB=0.974241;SGB=-0.692914;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,7,18;MQ=60 GT:PL:AD 1:255,0:0,25 -MN908947.3 23271 . C A 225.417 . DP=113;VDB=0.602922;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,87,25;MQ=60 GT:PL:AD 1:255,0:0,112 -MN908947.3 23403 . A G 225.417 . DP=103;VDB=0.311158;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,74,22;MQ=60 GT:PL:AD 1:255,0:0,96 -MN908947.3 23604 . C A 225.417 . DP=103;VDB=0.303274;SGB=-0.693147;MQSB=0.99457;MQ0F=0;AC=1;AN=1;DP4=0,0,71,25;MQ=59 GT:PL:AD 1:255,0:0,96 -MN908947.3 23709 . C T 225.422 . DP=105;VDB=0.072772;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,57,46;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 24506 . T G 225.417 . DP=85;VDB=0.0492644;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,15;MQ=60 GT:PL:AD 1:255,0:0,81 -MN908947.3 24914 . G C 225.417 . DP=120;VDB=0.741848;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,48;MQ=60 GT:PL:AD 1:255,0:0,114 -MN908947.3 25523 . G A 225.417 . DP=117;VDB=0.974641;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,67,43;MQ=60 GT:PL:AD 1:255,0:0,110 -MN908947.3 25693 . C A 225.417 . DP=50;VDB=0.0160805;SGB=-0.693146;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,13;MQ=60 GT:PL:AD 1:255,0:0,44 -MN908947.3 26606 . C T 225.417 . DP=78;VDB=0.00014612;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,59,15;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 27972 . C T 225.417 . DP=111;VDB=0.913367;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,64,38;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 28048 . G T 225.417 . DP=89;VDB=0.0584099;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,50,34;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 28111 . A G 228.412 . DP=77;VDB=0.999359;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,47,22;MQ=60 GT:PL:AD 1:255,0:1,69 -MN908947.3 28270 . TAAAA TAAA 5.97268 . INDEL;IDV=90;IMF=0.857143;DP=105;VDB=0.23186;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=20,11,53,21;MQ=60 GT:PL:AD 1:115,83:31,74 -MN908947.3 28280 . G C 225.417 . DP=90;VDB=0.00372887;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28281 . A T 225.417 . DP=90;VDB=0.00359238;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28282 . T A 225.417 . DP=91;VDB=0.00367371;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,61,24;MQ=60 GT:PL:AD 1:255,0:0,85 -MN908947.3 28817 . G T 228.414 . DP=75;VDB=0.460414;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,50,16;MQ=60 GT:PL:AD 1:255,0:1,66 -MN908947.3 28881 . G A 225.417 . DP=78;VDB=0.0391523;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28882 . G A 225.417 . DP=77;VDB=0.0433548;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28883 . G C 225.417 . DP=78;VDB=0.0387719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,42,31;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28977 . C T 225.417 . DP=74;VDB=0.318561;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,37;MQ=60 GT:PL:AD 1:255,0:0,69 diff --git a/benchmark/ERR5409159/ERR5409159.annotated.vcf b/benchmark/ERR5409159/ERR5409159.annotated.vcf deleted file mode 100644 index 5cbda42..0000000 --- a/benchmark/ERR5409159/ERR5409159.annotated.vcf +++ /dev/null @@ -1,78 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5409159/ERR5409159.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5409159.vcf; Date=Mon Jun 7 15:58:32 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:58:52 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5409159.normalized.vcf -; Date=Mon Jun 7 15:58:52 2021 -##bcftools/csqVersion=1.12+htslib-1.12 -##bcftools/csqCommand=csq --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --gff-annot /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.101.gff3 -o ERR5409159.annotated.vcf /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5409159/ERR5409159.normalized.vcf; Date=Mon Jun 7 15:58:54 2021 -##INFO= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=135;VDB=0.704481;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,104,20;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 913 . C T 225.417 . DP=120;VDB=0.0518176;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,92,19;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|216S|913C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|216S|913C>T GT:PL:AD:BCSQ 1:255,0:0,111:5 -MN908947.3 3037 . C T 225.417 . DP=123;VDB=0.549544;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,31;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|924F|3037C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|924F|3037C>T GT:PL:AD:BCSQ 1:255,0:0,117:5 -MN908947.3 3267 . C T 225.417 . DP=97;VDB=0.0093047;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,16;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1001T>1001I|3267C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1001T>1001I|3267C>T GT:PL:AD:BCSQ 1:255,0:0,92:5 -MN908947.3 5388 . C A 225.417 . DP=110;VDB=0.363775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,10;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1708A>1708D|5388C>A,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1708A>1708D|5388C>A GT:PL:AD:BCSQ 1:255,0:0,106:5 -MN908947.3 5986 . C T 225.417 . DP=90;VDB=0.0485343;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,12;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1907F|5986C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1907F|5986C>T GT:PL:AD:BCSQ 1:255,0:0,84:5 -MN908947.3 6954 . T C 225.417 . DP=24;VDB=0.0691992;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,10,8;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2230I>2230T|6954T>C,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2230I>2230T|6954T>C GT:PL:AD:BCSQ 1:255,0:0,18:5 -MN908947.3 8609 . T C 228.305 . DP=51;VDB=2.59948e-08;SGB=-0.693145;RPB=0.85;MQB=1;MQSB=1;BQB=0.9625;MQ0F=0;AC=1;AN=1;DP4=1,1,24,16;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2782F>2782L|8609T>C,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2782F>2782L|8609T>C GT:PL:AD:BCSQ 1:255,0:2,40:5 -MN908947.3 11287 . GTCTGGTTTT G 228.394 . INDEL;IDV=102;IMF=0.944444;DP=108;VDB=0.00631574;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=4,5,81,18;MQ=60;BCSQ=inframe_deletion|ORF1ab|ENSSAST00005000003|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G,inframe_deletion|ORF1ab|ENSSAST00005000002|protein_coding|+|3674LSGF>3674L|11287GTCTGGTTTT>G GT:PL:AD:BCSQ 1:255,0:9,99:5 -MN908947.3 13297 . C T 225.417 . DP=113;VDB=0.00594524;SGB=-0.693147;MQSB=0.998176;MQ0F=0;AC=1;AN=1;DP4=0,0,93,12;MQ=59;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|4344D|13297C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4344D|13297C>T GT:PL:AD:BCSQ 1:255,0:0,105:5 -MN908947.3 13763 . G T 225.417 . DP=129;VDB=0.972602;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,107,17;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|4500V>4497L|13763G>T GT:PL:AD:BCSQ 1:255,0:0,124:1 -MN908947.3 14408 . C T 225.417 . DP=123;VDB=0.210093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,88,24;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4715L|14408C>T GT:PL:AD:BCSQ 1:255,0:0,112:1 -MN908947.3 14676 . C T 225.417 . DP=112;VDB=0.0137719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,89,17;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|4804P>4801L|14676C>T GT:PL:AD:BCSQ 1:255,0:0,106:1 -MN908947.3 15279 . C T 225.417 . DP=92;VDB=0.108955;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,12;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5005T>5002I|15279C>T GT:PL:AD:BCSQ 1:255,0:0,89:1 -MN908947.3 16176 . T C 225.417 . DP=93;VDB=0.999997;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,10;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5304L>5301P|16176T>C GT:PL:AD:BCSQ 1:255,0:0,87:1 -MN908947.3 17615 . A G 225.417 . DP=118;VDB=0.16253;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,23;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5784S>5781G|17615A>G GT:PL:AD:BCSQ 1:255,0:0,113:1 -MN908947.3 21764 . ATACATG A 228.41 . INDEL;IDV=80;IMF=0.987654;DP=81;VDB=3.77053e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,62,18;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|68IHV>68I|21764ATACATG>A GT:PL:AD:BCSQ 1:255,0:1,80:1 -MN908947.3 21990 . TTTA T 228.326 . INDEL;IDV=37;IMF=0.860465;DP=43;VDB=0.0012936;SGB=-0.693139;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,25,11;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|143VYY>141V|21990TTTA>T+21994TTAC>T GT:PL:AD:BCSQ 1:255,0:7,36:1 -MN908947.3 21994 . TTAC T 180.281 . INDEL;IDV=1;IMF=0.025;DP=40;VDB=0.0144848;SGB=-0.693132;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,4,24,10;MQ=60;BCSQ=@21990 GT:PL:AD:BCSQ 1:207,0:6,34:1 -MN908947.3 23063 . A T 225.417 . DP=73;VDB=0.512093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,29;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|501N>497Y|23063A>T GT:PL:AD:BCSQ 1:255,0:0,65:1 -MN908947.3 23271 . C A 225.417 . DP=126;VDB=0.62606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,106,15;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|570A>566D|23271C>A GT:PL:AD:BCSQ 1:255,0:0,121:1 -MN908947.3 23403 . A G 225.417 . DP=109;VDB=0.440101;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,8;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|614D>610G|23403A>G GT:PL:AD:BCSQ 1:255,0:0,104:1 -MN908947.3 23604 . C A 225.417 . DP=124;VDB=0.0588215;SGB=-0.693147;MQSB=0.998441;MQ0F=0;AC=1;AN=1;DP4=0,0,105,13;MQ=59;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|681P>677H|23604C>A GT:PL:AD:BCSQ 1:255,0:0,118:1 -MN908947.3 23709 . C T 225.417 . DP=112;VDB=0.0814539;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,26;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|716T>712I|23709C>T GT:PL:AD:BCSQ 1:255,0:0,108:1 -MN908947.3 24399 . G A 228.372 . DP=94;VDB=9.53254e-05;SGB=-0.693147;RPB=0.0135686;MQB=1;MQSB=1;BQB=0.0414312;MQ0F=0;AC=1;AN=1;DP4=3,0,69,17;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|946G>942E|24399G>A GT:PL:AD:BCSQ 1:255,0:3,86:1 -MN908947.3 24506 . T G 225.417 . DP=99;VDB=0.00738591;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,15;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|982S>978A|24506T>G GT:PL:AD:BCSQ 1:255,0:0,94:1 -MN908947.3 24914 . G C 225.417 . DP=128;VDB=0.670937;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|1118D>1114H|24914G>C GT:PL:AD:BCSQ 1:255,0:0,118:1 -MN908947.3 26730 . G C 225.417 . DP=128;VDB=0.910743;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,111,13;MQ=60;BCSQ=missense|M|ENSSAST00005000007|protein_coding|+|70V>70L|26730G>C GT:PL:AD:BCSQ 1:255,0:0,124:1 -MN908947.3 27972 . C T 225.417 . DP=126;VDB=0.369513;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,100,18;MQ=60;BCSQ=stop_gained|ORF8|ENSSAST00005000008|protein_coding|+|27Q>27*|27972C>T GT:PL:AD:BCSQ 1:255,0:0,118:1 -MN908947.3 28048 . G T 225.417 . DP=109;VDB=0.0116576;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,17;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|52R>52I|28048G>T GT:PL:AD:BCSQ 1:255,0:0,103:1 -MN908947.3 28111 . A G 225.417 . DP=94;VDB=0.898709;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,68,15;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|73Y>73C|28111A>G GT:PL:AD:BCSQ 1:255,0:0,83:1 -MN908947.3 28270 . TA T 12.924 . INDEL;IDV=91;IMF=0.81982;DP=111;VDB=0.979327;SGB=-0.693147;MQSB=0.997581;MQ0F=0;AC=1;AN=1;DP4=24,5,70,12;MQ=59;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:99,59:29,82 -MN908947.3 28280 . G C 225.417 . DP=87;VDB=0.0113614;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|3D>3L|28280G>C+28281A>T+28282T>A GT:PL:AD:BCSQ 1:255,0:0,86:1 -MN908947.3 28281 . A T 225.417 . DP=87;VDB=0.0138443;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,86:1 -MN908947.3 28282 . T A 225.417 . DP=88;VDB=0.0151775;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:0,86:1 -MN908947.3 28881 . G A 225.417 . DP=82;VDB=0.152639;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|203R>203K|28881G>A+28882G>A GT:PL:AD:BCSQ 1:255,0:0,74:1 -MN908947.3 28882 . G A 225.417 . DP=81;VDB=0.13136;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,32;MQ=60;BCSQ=@28881 GT:PL:AD:BCSQ 1:255,0:0,73:1 -MN908947.3 28883 . G C 225.417 . DP=81;VDB=0.15109;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|204G>204R|28883G>C GT:PL:AD:BCSQ 1:255,0:0,74:1 -MN908947.3 28977 . C T 225.417 . DP=46;VDB=0.000220985;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,17,24;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|235S>235F|28977C>T GT:PL:AD:BCSQ 1:255,0:0,41:1 -MN908947.3 29311 . C T 225.417 . DP=85;VDB=2.66274e-09;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,18;MQ=60;BCSQ=synonymous|N|ENSSAST00005000005|protein_coding|+|346F|29311C>T GT:PL:AD:BCSQ 1:255,0:0,80:1 -MN908947.3 29587 . G A 228.267 . DP=80;VDB=0.00170351;SGB=-0.693147;RPB=0.847977;MQB=1;MQSB=1;BQB=0.346711;MQ0F=0;AC=1;AN=1;DP4=5,1,52,16;MQ=60;BCSQ=synonymous|ORF10|ENSSAST00005000013|protein_coding|+|10P|29587G>A GT:PL:AD:BCSQ 1:255,0:6,68:1 diff --git a/benchmark/ERR5409159/ERR5409159.normalized.vcf b/benchmark/ERR5409159/ERR5409159.normalized.vcf deleted file mode 100644 index 946ce1f..0000000 --- a/benchmark/ERR5409159/ERR5409159.normalized.vcf +++ /dev/null @@ -1,74 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5409159/ERR5409159.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5409159.vcf; Date=Mon Jun 7 15:58:32 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 15:58:52 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5409159.normalized.vcf -; Date=Mon Jun 7 15:58:52 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=135;VDB=0.704481;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,104,20;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 913 . C T 225.417 . DP=120;VDB=0.0518176;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,92,19;MQ=60 GT:PL:AD 1:255,0:0,111 -MN908947.3 3037 . C T 225.417 . DP=123;VDB=0.549544;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,31;MQ=60 GT:PL:AD 1:255,0:0,117 -MN908947.3 3267 . C T 225.417 . DP=97;VDB=0.0093047;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,16;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 5388 . C A 225.417 . DP=110;VDB=0.363775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,10;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 5986 . C T 225.417 . DP=90;VDB=0.0485343;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,12;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 6954 . T C 225.417 . DP=24;VDB=0.0691992;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,10,8;MQ=60 GT:PL:AD 1:255,0:0,18 -MN908947.3 8609 . T C 228.305 . DP=51;VDB=2.59948e-08;SGB=-0.693145;RPB=0.85;MQB=1;MQSB=1;BQB=0.9625;MQ0F=0;AC=1;AN=1;DP4=1,1,24,16;MQ=60 GT:PL:AD 1:255,0:2,40 -MN908947.3 11287 . GTCTGGTTTT G 228.394 . INDEL;IDV=102;IMF=0.944444;DP=108;VDB=0.00631574;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=4,5,81,18;MQ=60 GT:PL:AD 1:255,0:9,99 -MN908947.3 13297 . C T 225.417 . DP=113;VDB=0.00594524;SGB=-0.693147;MQSB=0.998176;MQ0F=0;AC=1;AN=1;DP4=0,0,93,12;MQ=59 GT:PL:AD 1:255,0:0,105 -MN908947.3 13763 . G T 225.417 . DP=129;VDB=0.972602;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,107,17;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 14408 . C T 225.417 . DP=123;VDB=0.210093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,88,24;MQ=60 GT:PL:AD 1:255,0:0,112 -MN908947.3 14676 . C T 225.417 . DP=112;VDB=0.0137719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,89,17;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 15279 . C T 225.417 . DP=92;VDB=0.108955;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,12;MQ=60 GT:PL:AD 1:255,0:0,89 -MN908947.3 16176 . T C 225.417 . DP=93;VDB=0.999997;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,10;MQ=60 GT:PL:AD 1:255,0:0,87 -MN908947.3 17615 . A G 225.417 . DP=118;VDB=0.16253;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,23;MQ=60 GT:PL:AD 1:255,0:0,113 -MN908947.3 21764 . ATACATG A 228.41 . INDEL;IDV=80;IMF=0.987654;DP=81;VDB=3.77053e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,62,18;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT GT:PL:AD 1:255,0:1,80 -MN908947.3 21990 . TTTA T 228.326 . INDEL;IDV=37;IMF=0.860465;DP=43;VDB=0.0012936;SGB=-0.693139;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,25,11;MQ=60;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA GT:PL:AD 1:255,0:7,36 -MN908947.3 21994 . TTAC T 180.281 . INDEL;IDV=1;IMF=0.025;DP=40;VDB=0.0144848;SGB=-0.693132;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,4,24,10;MQ=60 GT:PL:AD 1:207,0:6,34 -MN908947.3 23063 . A T 225.417 . DP=73;VDB=0.512093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,29;MQ=60 GT:PL:AD 1:255,0:0,65 -MN908947.3 23271 . C A 225.417 . DP=126;VDB=0.62606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,106,15;MQ=60 GT:PL:AD 1:255,0:0,121 -MN908947.3 23403 . A G 225.417 . DP=109;VDB=0.440101;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,8;MQ=60 GT:PL:AD 1:255,0:0,104 -MN908947.3 23604 . C A 225.417 . DP=124;VDB=0.0588215;SGB=-0.693147;MQSB=0.998441;MQ0F=0;AC=1;AN=1;DP4=0,0,105,13;MQ=59 GT:PL:AD 1:255,0:0,118 -MN908947.3 23709 . C T 225.417 . DP=112;VDB=0.0814539;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,26;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 24399 . G A 228.372 . DP=94;VDB=9.53254e-05;SGB=-0.693147;RPB=0.0135686;MQB=1;MQSB=1;BQB=0.0414312;MQ0F=0;AC=1;AN=1;DP4=3,0,69,17;MQ=60 GT:PL:AD 1:255,0:3,86 -MN908947.3 24506 . T G 225.417 . DP=99;VDB=0.00738591;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,15;MQ=60 GT:PL:AD 1:255,0:0,94 -MN908947.3 24914 . G C 225.417 . DP=128;VDB=0.670937;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 26730 . G C 225.417 . DP=128;VDB=0.910743;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,111,13;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 27972 . C T 225.417 . DP=126;VDB=0.369513;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,100,18;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 28048 . G T 225.417 . DP=109;VDB=0.0116576;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,17;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 28111 . A G 225.417 . DP=94;VDB=0.898709;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,68,15;MQ=60 GT:PL:AD 1:255,0:0,83 -MN908947.3 28270 . TA T 12.924 . INDEL;IDV=91;IMF=0.81982;DP=111;VDB=0.979327;SGB=-0.693147;MQSB=0.997581;MQ0F=0;AC=1;AN=1;DP4=24,5,70,12;MQ=59;OLD_CLUMPED=MN908947.3|28270|TAAAA|TAAA GT:PL:AD 1:99,59:29,82 -MN908947.3 28280 . G C 225.417 . DP=87;VDB=0.0113614;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28281 . A T 225.417 . DP=87;VDB=0.0138443;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28282 . T A 225.417 . DP=88;VDB=0.0151775;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28881 . G A 225.417 . DP=82;VDB=0.152639;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 28882 . G A 225.417 . DP=81;VDB=0.13136;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,32;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28883 . G C 225.417 . DP=81;VDB=0.15109;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 28977 . C T 225.417 . DP=46;VDB=0.000220985;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,17,24;MQ=60 GT:PL:AD 1:255,0:0,41 -MN908947.3 29311 . C T 225.417 . DP=85;VDB=2.66274e-09;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,18;MQ=60 GT:PL:AD 1:255,0:0,80 -MN908947.3 29587 . G A 228.267 . DP=80;VDB=0.00170351;SGB=-0.693147;RPB=0.847977;MQB=1;MQSB=1;BQB=0.346711;MQ0F=0;AC=1;AN=1;DP4=5,1,52,16;MQ=60 GT:PL:AD 1:255,0:6,68 diff --git a/benchmark/ERR5409159/ERR5409159.preprocessed.gatk.vcf b/benchmark/ERR5409159/ERR5409159.preprocessed.gatk.vcf deleted file mode 100644 index 5a57951..0000000 --- a/benchmark/ERR5409159/ERR5409159.preprocessed.gatk.vcf +++ /dev/null @@ -1,66 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 82329.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.659;DP=2827;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.05;ReadPosRankSum=1.283;SOR=0.260 GT:AD:DP:GQ:PL 1:1,2739:2740:99:82339,0 -MN908947.3 913 . C T 85830.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.191;DP=2815;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.54;ReadPosRankSum=1.486;SOR=1.000 GT:AD:DP:GQ:PL 1:5,2716:2721:99:85840,0 -MN908947.3 3037 . C T 70669.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.463;DP=2314;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.02;ReadPosRankSum=-1.567;SOR=0.363 GT:AD:DP:GQ:PL 1:1,2277:2278:99:70679,0 -MN908947.3 3267 . C T 45703.04 . AC=1;AF=1.00;AN=1;DP=1544;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.01;QD=30.23;SOR=1.383 GT:AD:DP:GQ:PL 1:0,1512:1512:99:45713,0 -MN908947.3 5388 . C A 86240.04 . AC=1;AF=1.00;AN=1;DP=2626;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.21;SOR=1.641 GT:AD:DP:GQ:PL 1:0,2597:2597:99:86250,0 -MN908947.3 5986 . C T 43407.04 . AC=1;AF=1.00;AN=1;DP=1311;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.26;SOR=2.076 GT:AD:DP:GQ:PL 1:0,1305:1305:99:43417,0 -MN908947.3 6954 . T C 1077.04 . AC=1;AF=1.00;AN=1;DP=36;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.92;SOR=1.371 GT:AD:DP:GQ:PL 1:0,36:36:99:1087,0 -MN908947.3 8609 . T C 8822.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.703;DP=267;FS=6.639;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.42;ReadPosRankSum=1.002;SOR=2.593 GT:AD:DP:GQ:PL 1:4,260:264:99:8832,0 -MN908947.3 11287 . GTCTGGTTTT G 70149.04 . AC=1;AF=1.00;AN=1;DP=2148;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.34;SOR=1.798 GT:AD:DP:GQ:PL 1:0,2043:2043:99:91480,0 -MN908947.3 13297 . C T 99865.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.939;DP=3086;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.32;ReadPosRankSum=0.949;SOR=1.046 GT:AD:DP:GQ:PL 1:1,2996:2997:99:99875,0 -MN908947.3 13763 . G T 59123.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.091;DP=2110;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.70;ReadPosRankSum=0.056;SOR=1.108 GT:AD:DP:GQ:PL 1:14,2046:2060:99:59133,0 -MN908947.3 14408 . C T 87193.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.185;DP=2801;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.41;ReadPosRankSum=-0.465;SOR=0.722 GT:AD:DP:GQ:PL 1:2,2688:2690:99:87203,0 -MN908947.3 14676 . C T 60005.04 . AC=1;AF=1.00;AN=1;DP=1923;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.45;SOR=1.620 GT:AD:DP:GQ:PL 1:0,1908:1908:99:60015,0 -MN908947.3 15279 . C T 81146.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.924;DP=2539;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.92;ReadPosRankSum=-0.499;SOR=0.622 GT:AD:DP:GQ:PL 1:1,2464:2465:99:81156,0 -MN908947.3 16176 . T C 77199.04 . AC=1;AF=1.00;AN=1;DP=2351;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=34.74;SOR=0.825 GT:AD:DP:GQ:PL 1:0,2222:2222:99:77209,0 -MN908947.3 17615 . A G 123422.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=2.143;DP=3862;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.85;ReadPosRankSum=-2.416;SOR=0.691 GT:AD:DP:GQ:PL 1:3,3754:3757:99:123432,0 -MN908947.3 21764 . ATACATG A 39500.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.120;DP=1307;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.37;MQRankSum=0.270;QD=32.17;ReadPosRankSum=-1.281;SOR=1.328 GT:AD:DP:GQ:PL 1:2,1226:1228:99:51600,0 -MN908947.3 21990 . TTTA T 13667.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.658;DP=419;FS=4.024;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=34.95;ReadPosRankSum=1.066;SOR=2.581 GT:AD:DP:GQ:PL 1:2,389:391:99:13677,0 -MN908947.3 23063 . A T 10716.04 . AC=1;AF=1.00;AN=1;DP=370;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.12;SOR=1.359 GT:AD:DP:GQ:PL 1:0,368:368:99:10726,0 -MN908947.3 23271 . C A 108824.04 . AC=1;AF=1.00;AN=1;DP=3394;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.57;SOR=1.363 GT:AD:DP:GQ:PL 1:0,3341:3341:99:108834,0 -MN908947.3 23403 . A G 98426.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.468;DP=3147;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.97;ReadPosRankSum=-0.612;SOR=0.236 GT:AD:DP:GQ:PL 1:2,3077:3079:99:98436,0 -MN908947.3 23604 . C A 103968.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.973;DP=3261;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.26;ReadPosRankSum=-1.114;SOR=0.981 GT:AD:DP:GQ:PL 1:1,3222:3223:99:103978,0 -MN908947.3 23709 . C T 92114.04 . AC=1;AF=1.00;AN=1;DP=2896;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.29;SOR=1.535 GT:AD:DP:GQ:PL 1:0,2853:2853:99:92124,0 -MN908947.3 24399 . G A 39812.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.334;DP=1501;FS=4.816;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.52;ReadPosRankSum=3.226;SOR=1.494 GT:AD:DP:GQ:PL 1:16,1380:1396:99:39822,0 -MN908947.3 24506 . T G 55281.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.321;DP=1683;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.30;ReadPosRankSum=1.555;SOR=0.548 GT:AD:DP:GQ:PL 1:2,1658:1660:99:55291,0 -MN908947.3 24914 . G C 139524.04 . AC=1;AF=1.00;AN=1;DP=4335;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.07;SOR=1.521 GT:AD:DP:GQ:PL 1:0,4219:4219:99:139534,0 -MN908947.3 26730 . G C 145133.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.208;DP=4461;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=-0.108;QD=33.14;ReadPosRankSum=0.625;SOR=0.704 GT:AD:DP:GQ:PL 1:4,4376:4380:99:145143,0 -MN908947.3 27972 . C T 102735.04 . AC=1;AF=1.00;AN=1;DP=3241;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=32.54;SOR=0.887 GT:AD:DP:GQ:PL 1:0,3157:3157:99:102745,0 -MN908947.3 28048 . G T 83240.04 . AC=1;AF=1.00;AN=1;DP=2614;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=31.90;SOR=1.344 GT:AD:DP:GQ:PL 1:0,2609:2609:99:83250,0 -MN908947.3 28111 . A G 65738.04 . AC=1;AF=1.00;AN=1;DP=2099;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.25;SOR=0.805 GT:AD:DP:GQ:PL 1:0,1977:1977:99:65748,0 -MN908947.3 28270 . TA T 152065.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.928;DP=3654;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;MQRankSum=0.000;QD=32.56;ReadPosRankSum=1.516;SOR=0.237 GT:AD:DP:GQ:PL 1:1,3428:3429:99:152075,0 -MN908947.3 28280 . G C 148218.04 . AC=1;AF=1.00;AN=1;DP=3312;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=29.94;SOR=0.728 GT:AD:DP:GQ:PL 1:0,3312:3312:99:148228,0 -MN908947.3 28281 . A T 147944.04 . AC=1;AF=1.00;AN=1;DP=3320;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=29.33;SOR=0.723 GT:AD:DP:GQ:PL 1:0,3304:3304:99:147954,0 -MN908947.3 28282 . T A 147997.04 . AC=1;AF=1.00;AN=1;DP=3348;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=31.72;SOR=0.723 GT:AD:DP:GQ:PL 1:0,3306:3306:99:148007,0 -MN908947.3 28881 . G A 8219.04 . AC=1;AF=1.00;AN=1;DP=288;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.04;SOR=1.008 GT:AD:DP:GQ:PL 1:0,283:283:99:12665,0 -MN908947.3 28882 . G A 8318.04 . AC=1;AF=1.00;AN=1;DP=288;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.39;SOR=1.008 GT:AD:DP:GQ:PL 1:0,283:283:99:12665,0 -MN908947.3 28883 . G C 8442.04 . AC=1;AF=1.00;AN=1;DP=292;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.83;SOR=1.008 GT:AD:DP:GQ:PL 1:0,283:283:99:12665,0 -MN908947.3 28977 . C T 5035.04 . AC=1;AF=1.00;AN=1;DP=161;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=33.34;SOR=2.515 GT:AD:DP:GQ:PL 1:0,151:151:99:5045,0 -MN908947.3 29311 . C T 59229.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.386;DP=1803;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.37;ReadPosRankSum=1.182;SOR=0.328 GT:AD:DP:GQ:PL 1:8,1767:1775:99:60722,0 -MN908947.3 29587 . G A 23496.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-2.316;DP=766;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.79;ReadPosRankSum=0.554;SOR=0.414 GT:AD:DP:GQ:PL 1:6,757:763:99:23506,0 diff --git a/benchmark/ERR5409159/ERR5409159.preprocessed.ivar.tsv b/benchmark/ERR5409159/ERR5409159.preprocessed.ivar.tsv deleted file mode 100644 index 6493f1a..0000000 --- a/benchmark/ERR5409159/ERR5409159.preprocessed.ivar.tsv +++ /dev/null @@ -1,114 +0,0 @@ -REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA -MN908947.3 89 T -N 735 3 48 61 0 20 0.0634096 962 1.24151e-13 TRUE NA NA NA NA NA -MN908947.3 104 T -N 866 5 49 73 0 20 0.0636998 1146 4.48675e-16 TRUE NA NA NA NA NA -MN908947.3 241 C T 1 1 38 1860 464 60 0.999463 1861 0 TRUE NA NA NA NA NA -MN908947.3 295 G A 1545 875 52 116 66 52 0.0698374 1661 1.08236e-46 TRUE CDS:ENSSASP00005000003 GAG E GAA E -MN908947.3 295 G A 1545 875 52 116 66 52 0.0698374 1661 1.08236e-46 TRUE CDS:ENSSASP00005000002 GAG E GAA E -MN908947.3 913 C T 4 2 56 2190 1107 55 0.998177 2194 0 TRUE CDS:ENSSASP00005000003 TCC S TCT S -MN908947.3 913 C T 4 2 56 2190 1107 55 0.998177 2194 0 TRUE CDS:ENSSASP00005000002 TCC S TCT S -MN908947.3 2824 T C 103 76 46 4 4 35 0.0373832 107 0.0382805 FALSE CDS:ENSSASP00005000003 CTT L CTC L -MN908947.3 2824 T C 103 76 46 4 4 35 0.0373832 107 0.0382805 FALSE CDS:ENSSASP00005000002 CTT L CTC L -MN908947.3 3037 C T 1 1 38 1590 588 56 0.999371 1591 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 3037 C T 1 1 38 1590 588 56 0.999371 1591 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 3267 C T 0 0 0 1013 7 57 1 1013 0 TRUE CDS:ENSSASP00005000003 ACT T ATT I -MN908947.3 3267 C T 0 0 0 1013 7 57 1 1013 0 TRUE CDS:ENSSASP00005000002 ACT T ATT I -MN908947.3 3323 G -N 1148 150 58 104 0 20 0.0579387 1795 2.69829e-25 TRUE NA NA NA NA NA -MN908947.3 3550 A C 305 0 50 54 0 48 0.150418 359 1.05874e-21 TRUE CDS:ENSSASP00005000003 GGA G GGC G -MN908947.3 3550 A C 305 0 50 54 0 48 0.150418 359 1.05874e-21 TRUE CDS:ENSSASP00005000002 GGA G GGC G -MN908947.3 3559 A G 346 0 49 84 0 50 0.195349 430 5.36864e-34 TRUE CDS:ENSSASP00005000003 AAA K AAG K -MN908947.3 3559 A G 346 0 49 84 0 50 0.195349 430 5.36864e-34 TRUE CDS:ENSSASP00005000002 AAA K AAG K -MN908947.3 3977 G -N 620 218 53 69 0 20 0.0765816 901 2.11544e-17 TRUE NA NA NA NA NA -MN908947.3 5388 C A 0 0 0 2169 5 53 0.999079 2171 0 TRUE CDS:ENSSASP00005000003 GCT A GAT D -MN908947.3 5388 C A 0 0 0 2169 5 53 0.999079 2171 0 TRUE CDS:ENSSASP00005000002 GCT A GAT D -MN908947.3 5857 G A 1861 951 55 93 51 53 0.0475947 1954 4.931e-38 TRUE CDS:ENSSASP00005000003 ACG T ACA T -MN908947.3 5857 G A 1861 951 55 93 51 53 0.0475947 1954 4.931e-38 TRUE CDS:ENSSASP00005000002 ACG T ACA T -MN908947.3 5986 C T 0 0 0 988 2 51 1 988 0 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 5986 C T 0 0 0 988 2 51 1 988 0 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 6954 T C 0 0 0 25 12 54 1 25 1.13678e-17 TRUE CDS:ENSSASP00005000003 ATA I ACA T -MN908947.3 6954 T C 0 0 0 25 12 54 1 25 1.13678e-17 TRUE CDS:ENSSASP00005000002 ATA I ACA T -MN908947.3 6973 A T 24 11 57 1 1 21 0.04 25 0.403226 FALSE CDS:ENSSASP00005000003 TTA L TTT F -MN908947.3 6973 A T 24 11 57 1 1 21 0.04 25 0.403226 FALSE CDS:ENSSASP00005000002 TTA L TTT F -MN908947.3 7000 C G 23 14 49 1 0 76 0.0416667 24 0.421053 FALSE CDS:ENSSASP00005000003 TAC Y TAG * -MN908947.3 7000 C G 23 14 49 1 0 76 0.0416667 24 0.421053 FALSE CDS:ENSSASP00005000002 TAC Y TAG * -MN908947.3 7731 A C 2127 5 53 168 0 50 0.0732026 2295 1.02558e-66 TRUE CDS:ENSSASP00005000003 TAC Y TCC S -MN908947.3 7731 A C 2127 5 53 168 0 50 0.0732026 2295 1.02558e-66 TRUE CDS:ENSSASP00005000002 TAC Y TCC S -MN908947.3 7949 A T 1803 1249 48 74 58 45 0.0394246 1877 6.96426e-28 TRUE CDS:ENSSASP00005000003 AGT S TGT C -MN908947.3 7949 A T 1803 1249 48 74 58 45 0.0394246 1877 6.96426e-28 TRUE CDS:ENSSASP00005000002 AGT S TGT C -MN908947.3 8035 G -N 1363 6 49 114 0 20 0.0625 1824 4.19655e-24 TRUE NA NA NA NA NA -MN908947.3 8609 T C 3 1 58 214 155 46 0.986175 217 1.33257e-139 TRUE CDS:ENSSASP00005000003 TTT F CTT L -MN908947.3 8609 T C 3 1 58 214 155 46 0.986175 217 1.33257e-139 TRUE CDS:ENSSASP00005000002 TTT F CTT L -MN908947.3 8882 A G 32 14 55 1 1 34 0.030303 33 0.383721 FALSE CDS:ENSSASP00005000003 ATA I GTA V -MN908947.3 8882 A G 32 14 55 1 1 34 0.030303 33 0.383721 FALSE CDS:ENSSASP00005000002 ATA I GTA V -MN908947.3 11074 C -N 1419 16 47 221 0 20 0.120567 1833 4.17781e-54 TRUE NA NA NA NA NA -MN908947.3 11287 G -NNNNNNNNN 1757 1029 52 2249 0 20 0.901764 2494 0 TRUE NA NA NA NA NA -MN908947.3 11288 T A 1 1 38 23 2 36 0.958333 24 1.00465e-51 TRUE CDS:ENSSASP00005000003 TCT S ACT T -MN908947.3 11288 T A 1 1 38 23 2 36 0.958333 24 1.00465e-51 TRUE CDS:ENSSASP00005000002 TCT S ACT T -MN908947.3 11291 G A 1 0 76 2 0 34 0.666667 3 7.06602e-06 TRUE CDS:ENSSASP00005000003 GGT G AGT S -MN908947.3 11291 G A 1 0 76 2 0 34 0.666667 3 7.06602e-06 TRUE CDS:ENSSASP00005000002 GGT G AGT S -MN908947.3 11296 T G 0 0 0 3 0 76 1 3 5.2117e-10 TRUE CDS:ENSSASP00005000003 TTT F TTG L -MN908947.3 11296 T G 0 0 0 3 0 76 1 3 5.2117e-10 TRUE CDS:ENSSASP00005000002 TTT F TTG L -MN908947.3 11600 A G 1522 684 48 195 139 47 0.11357 1717 3.45559e-74 TRUE CDS:ENSSASP00005000003 ATA I GTA V -MN908947.3 11600 A G 1522 684 48 195 139 47 0.11357 1717 3.45559e-74 TRUE CDS:ENSSASP00005000002 ATA I GTA V -MN908947.3 11630 T A 1241 445 48 136 99 46 0.0987654 1377 1.12397e-51 TRUE CDS:ENSSASP00005000003 TTT F ATT I -MN908947.3 11630 T A 1241 445 48 136 99 46 0.0987654 1377 1.12397e-51 TRUE CDS:ENSSASP00005000002 TTT F ATT I -MN908947.3 12028 G T 3280 327 60 214 17 59 0.0612303 3495 4.39216e-92 TRUE CDS:ENSSASP00005000003 ATG M ATT I -MN908947.3 12028 G T 3280 327 60 214 17 59 0.0612303 3495 4.39216e-92 TRUE CDS:ENSSASP00005000002 ATG M ATT I -MN908947.3 12462 C T 1623 245 45 95 0 46 0.0552969 1718 2.23527e-34 TRUE CDS:ENSSASP00005000003 ACA T ATA I -MN908947.3 12462 C T 1623 245 45 95 0 46 0.0552969 1718 2.23527e-34 TRUE CDS:ENSSASP00005000002 ACA T ATA I -MN908947.3 13297 C T 3 2 30 3309 1906 53 0.998793 3313 0 TRUE CDS:ENSSASP00005000003 GAC D GAT D -MN908947.3 13297 C T 3 2 30 3309 1906 53 0.998793 3313 0 TRUE CDS:ENSSASP00005000002 GAC D GAT D -MN908947.3 13402 T G 767 5 54 32 1 49 0.0400501 799 2.1075e-13 TRUE CDS:ENSSASP00005000003 TAT Y TAG * -MN908947.3 13402 T G 767 5 54 32 1 49 0.0400501 799 2.1075e-13 TRUE CDS:ENSSASP00005000002 TAT Y TAG * -MN908947.3 13572 T C 736 375 54 55 31 52 0.0695322 791 6.28532e-23 TRUE CDS:ENSSASP00005000002 GTT V GCT A -MN908947.3 13763 G T 9 1 60 1316 52 60 0.992459 1326 0 TRUE CDS:ENSSASP00005000002 GTG V TTG L -MN908947.3 14408 C T 1 0 76 2088 531 56 0.999521 2089 0 TRUE CDS:ENSSASP00005000002 CTA L TTA L -MN908947.3 14676 C T 0 0 0 1372 6 54 1 1372 0 TRUE CDS:ENSSASP00005000002 CCG P CTG L -MN908947.3 15279 C T 0 0 0 2195 11 54 1 2195 0 TRUE CDS:ENSSASP00005000002 ACC T ATC I -MN908947.3 15857 C T 2198 866 44 124 96 43 0.0534022 2322 2.41848e-44 TRUE CDS:ENSSASP00005000002 CTA L TTA L -MN908947.3 16176 T C 0 0 0 2397 711 47 1 2397 0 TRUE CDS:ENSSASP00005000002 CTT L CCT P -MN908947.3 16446 T C 1487 886 46 87 71 43 0.0552732 1574 3.55012e-32 TRUE CDS:ENSSASP00005000002 ATT I ACT T -MN908947.3 16878 A G 2116 6 56 288 2 56 0.1198 2404 5.94726e-121 TRUE CDS:ENSSASP00005000002 CAA Q CGA R -MN908947.3 17083 C T 2007 950 47 87 63 46 0.0415473 2094 9.92815e-33 TRUE CDS:ENSSASP00005000002 GAC D GAT D -MN908947.3 17615 A G 2 1 57 3493 1533 57 0.999428 3495 0 TRUE CDS:ENSSASP00005000002 AGC S GGC G -MN908947.3 18486 C T 2413 788 56 124 54 53 0.0488766 2537 1.47246e-51 TRUE CDS:ENSSASP00005000002 TCA S TTA L -MN908947.3 19820 C -NN 799 364 57 69 0 20 0.0559611 1233 1.24596e-16 TRUE NA NA NA NA NA -MN908947.3 20226 A T 32 20 46 1 1 34 0.030303 33 0.445946 FALSE CDS:ENSSASP00005000002 AAT N ATT I -MN908947.3 20295 T -N 9 0 50 1 0 20 0.0833333 12 0.47619 FALSE NA NA NA NA NA -MN908947.3 20362 T A 9 1 52 1 0 76 0.1 10 0.4 FALSE CDS:ENSSASP00005000002 GTT V GTA V -MN908947.3 20371 C A 9 1 58 1 0 57 0.1 10 0.4 FALSE CDS:ENSSASP00005000002 TAC Y TAA * -MN908947.3 20480 C G 28 6 38 2 0 34 0.0666667 30 0.230037 FALSE CDS:ENSSASP00005000002 CAT H GAT D -MN908947.3 21764 A -NNNNNN 975 10 55 1444 0 20 0.983651 1468 0 TRUE NA NA NA NA NA -MN908947.3 21770 G C 0 0 0 1 0 76 1 1 0.000691563 TRUE CDS:ENSSASP00005000004 GTC V CTC L -MN908947.3 21990 T -NNN 328 227 46 339 0 20 0.822816 412 1.143e-83 TRUE NA NA NA NA NA -MN908947.3 22642 C -NN 979 13 60 80 0 20 0.0506329 1580 2.67607e-19 TRUE NA NA NA NA NA -MN908947.3 22771 A -N 1073 355 61 77 0 20 0.0428492 1797 5.76617e-18 TRUE NA NA NA NA NA -MN908947.3 23063 A T 0 0 0 232 95 59 1 232 1.53848e-173 TRUE CDS:ENSSASP00005000004 AAT N TAT Y -MN908947.3 23271 C A 0 0 0 2822 10 58 1 2822 0 TRUE CDS:ENSSASP00005000004 GCT A GAT D -MN908947.3 23403 A G 1 1 38 2696 1265 56 0.999629 2697 0 TRUE CDS:ENSSASP00005000004 GAT D GGT G -MN908947.3 23604 C A 0 0 0 2610 103 56 0.999617 2611 0 TRUE CDS:ENSSASP00005000004 CCT P CAT H -MN908947.3 23709 C T 0 0 0 2320 1217 55 1 2320 0 TRUE CDS:ENSSASP00005000004 ACA T ATA I -MN908947.3 23818 T C 460 314 44 49 37 44 0.0962672 509 2.16211e-18 TRUE CDS:ENSSASP00005000004 CTT L CTC L -MN908947.3 24399 G A 13 3 37 1431 913 50 0.990997 1444 0 TRUE CDS:ENSSASP00005000004 GGA G GAA E -MN908947.3 24506 T G 1 0 31 1363 6 50 0.998535 1365 0 TRUE CDS:ENSSASP00005000004 TCA S GCA A -MN908947.3 24914 G C 0 0 0 3516 1718 55 1 3516 0 TRUE CDS:ENSSASP00005000004 GAC D CAC H -MN908947.3 26447 C T 589 324 53 72 40 53 0.108926 661 1.00136e-29 TRUE CDS:ENSSASP00005000010 TCT S TTT F -MN908947.3 26596 G T 2226 3 49 84 0 41 0.0363479 2311 1.18078e-31 TRUE CDS:ENSSASP00005000007 GGT G GTT V -MN908947.3 26730 G C 5 1 60 3845 1008 57 0.998442 3851 0 TRUE CDS:ENSSASP00005000007 GTT V CTT L -MN908947.3 27323 C T 2211 413 57 130 30 56 0.0555081 2342 2.53991e-54 TRUE CDS:ENSSASP00005000011 TCT S TTT F -MN908947.3 27792 T A 85 29 41 47 0 37 0.356061 132 1.32689e-18 TRUE CDS:ENSSASP00005000012 TTT F ATT I -MN908947.3 27972 C T 0 0 0 2463 719 57 0.999594 2464 0 TRUE CDS:ENSSASP00005000008 CAA Q TAA * -MN908947.3 28048 G T 0 0 0 1932 898 57 0.999483 1933 0 TRUE CDS:ENSSASP00005000008 AGA R ATA I -MN908947.3 28072 T A 1612 775 56 62 33 54 0.037037 1674 7.03628e-26 TRUE CDS:ENSSASP00005000008 TTG L TAG * -MN908947.3 28111 A G 0 0 0 1937 579 49 1 1937 0 TRUE CDS:ENSSASP00005000008 TAC Y TGC C -MN908947.3 28270 T -N 3254 606 56 4149 0 20 0.846735 4900 0 TRUE NA NA NA NA NA -MN908947.3 28280 G C 0 0 0 2859 912 51 1 2859 0 TRUE CDS:ENSSASP00005000005 GAT D CAT H -MN908947.3 28281 A T 0 0 0 2853 909 51 1 2853 0 TRUE CDS:ENSSASP00005000005 GAT D GTT V -MN908947.3 28282 T A 0 0 0 2897 930 52 1 2897 0 TRUE CDS:ENSSASP00005000005 GAT D GAA E -MN908947.3 28881 G A 0 0 0 180 67 52 1 180 6.65559e-128 TRUE CDS:ENSSASP00005000005 AGG R AAG K -MN908947.3 28882 G A 0 0 0 180 68 52 1 180 1.13171e-127 TRUE CDS:ENSSASP00005000005 AGG R AGA R -MN908947.3 28883 G C 0 0 0 179 67 52 1 179 2.74125e-127 TRUE CDS:ENSSASP00005000005 GGA G CGA R -MN908947.3 28977 C T 0 0 0 117 83 46 1 117 3.73386e-79 TRUE CDS:ENSSASP00005000005 TCT S TTT F -MN908947.3 29017 G A 940 55 43 38 0 39 0.0388548 978 1.64634e-12 TRUE CDS:ENSSASP00005000005 AAG K AAA K -MN908947.3 29311 C T 8 6 46 1842 1282 48 0.995676 1850 0 TRUE CDS:ENSSASP00005000005 TTC F TTT F -MN908947.3 29373 A T 1 0 38 1 1 34 0.5 2 0.666667 FALSE CDS:ENSSASP00005000005 GAG E GTG V -MN908947.3 29587 G A 7 1 34 544 0 53 0.987296 551 0 TRUE CDS:ENSSASP00005000013 CCG P CCA P diff --git a/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter01.vcf b/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter01.vcf deleted file mode 100644 index 5da1e65..0000000 --- a/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter01.vcf +++ /dev/null @@ -1,66 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5409159/ERR5409159.preprocessed.lofreq.vcf ERR5409159/ERR5409159.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.1' ./ERR5409159/ERR5409159.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:31 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 49314 PASS DP=3072;AF=0.98763;SB=0;DP4=1,1,1396,1666 -MN908947.3 913 . C T 49314 PASS DP=3286;AF=0.987827;SB=0;DP4=2,4,1084,2191 -MN908947.3 3037 . C T 49314 PASS DP=2417;AF=0.994621;SB=0;DP4=0,1,995,1418 -MN908947.3 3267 . C T 49314 PASS DP=1566;AF=0.993614;SB=0;DP4=0,0,1009,557 -MN908947.3 3550 . A C 1643 PASS DP=481;AF=0.14553;SB=1;DP4=305,106,54,16 -MN908947.3 3559 . A G 2829 PASS DP=578;AF=0.195502;SB=0;DP4=346,119,84,29 -MN908947.3 5388 . C A 49314 PASS DP=3133;AF=0.991701;SB=0;DP4=0,0,2174,955 -MN908947.3 5986 . C T 49202 PASS DP=1352;AF=0.997041;SB=0;DP4=0,0,988,364 -MN908947.3 6954 . T C 1324 PASS DP=37;AF=1;SB=0;DP4=0,0,13,24 -MN908947.3 8609 . T C 9754 PASS DP=277;AF=0.971119;SB=2;DP4=2,4,59,211 -MN908947.3 11074 . CT C 3906 PASS DP=1813;AF=0.121346;SB=0;DP4=1239,358,170,50;INDEL;HRUN=8 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=2270;AF=0.988106;SB=13;DP4=85,158,644,1599;INDEL;HRUN=1 -MN908947.3 11600 . A G 5642 PASS DP=2229;AF=0.111709;SB=91;DP4=836,1143,56,193 -MN908947.3 13297 . C T 49314 PASS DP=4710;AF=0.992144;SB=2;DP4=1,1,1399,3303 -MN908947.3 13763 . G T 49314 PASS DP=2158;AF=0.984245;SB=0;DP4=8,6,1266,873 -MN908947.3 14408 . C T 49314 PASS DP=3189;AF=0.993728;SB=0;DP4=1,1,1559,1626 -MN908947.3 14676 . C T 49314 PASS DP=2035;AF=0.987224;SB=0;DP4=1,0,1373,658 -MN908947.3 15279 . C T 49314 PASS DP=3237;AF=0.991968;SB=0;DP4=2,0,2190,1042 -MN908947.3 16176 . T C 49314 PASS DP=3111;AF=0.992607;SB=0;DP4=1,0,1692,1415 -MN908947.3 16878 . A G 10324 PASS DP=3646;AF=0.12068;SB=1;DP4=2115,1087,287,155 -MN908947.3 17615 . A G 49314 PASS DP=5442;AF=0.991731;SB=0;DP4=1,3,1959,3478 -MN908947.3 21764 . ATACATG A 49314 PASS DP=1461;AF=0.985626;SB=25;DP4=8,15,966,474;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 12904 PASS DP=406;AF=0.832512;SB=14;DP4=11,62,90,248;INDEL;HRUN=3 -MN908947.3 23063 . A T 13330 PASS DP=370;AF=0.991892;SB=0;DP4=0,0,136,234 -MN908947.3 23271 . C A 49314 PASS DP=4448;AF=0.990108;SB=0;DP4=0,0,2825,1620 -MN908947.3 23403 . A G 49314 PASS DP=4117;AF=0.992956;SB=2;DP4=0,2,1427,2688 -MN908947.3 23604 . C A 49314 PASS DP=3999;AF=0.991498;SB=4;DP4=0,1,2511,1485 -MN908947.3 23709 . C T 49314 PASS DP=3425;AF=0.995328;SB=4;DP4=1,0,1101,2321 -MN908947.3 24399 . G A 49314 PASS DP=1954;AF=0.986694;SB=32;DP4=11,5,512,1424 -MN908947.3 24506 . T G 49314 PASS DP=1863;AF=0.987118;SB=0;DP4=2,0,1365,494 -MN908947.3 24914 . G C 49314 PASS DP=5255;AF=0.992579;SB=0;DP4=0,0,1796,3457 -MN908947.3 26447 . C T 2369 PASS DP=952;AF=0.109244;SB=0;DP4=263,583,32,74 -MN908947.3 26730 . G C 49314 PASS DP=5993;AF=0.992491;SB=0;DP4=4,4,2840,3141 -MN908947.3 27972 . C T 49314 PASS DP=3736;AF=0.993308;SB=0;DP4=0,0,1746,1988 -MN908947.3 28048 . G T 49314 PASS DP=2949;AF=0.993557;SB=0;DP4=0,0,1033,1912 -MN908947.3 28111 . A G 49314 PASS DP=2623;AF=0.99085;SB=0;DP4=0,0,1357,1263 -MN908947.3 28270 . TA T 49314 PASS DP=4876;AF=0.849262;SB=179;DP4=517,231,2147,1994;INDEL;HRUN=4 -MN908947.3 28280 . G C 49314 PASS DP=3955;AF=0.995196;SB=0;DP4=0,0,1962,1992 -MN908947.3 28281 . A T 49314 PASS DP=3955;AF=0.994185;SB=0;DP4=0,0,1960,1991 -MN908947.3 28282 . T A 49314 PASS DP=4030;AF=0.996774;SB=0;DP4=0,0,1982,2048 -MN908947.3 28881 . G A 9486 PASS DP=258;AF=1;SB=0;DP4=0,0,113,145 -MN908947.3 28882 . G A 9398 PASS DP=257;AF=0.992218;SB=0;DP4=0,0,112,144 -MN908947.3 28883 . G C 9426 PASS DP=257;AF=0.992218;SB=0;DP4=0,0,112,143 -MN908947.3 28977 . C T 5433 PASS DP=152;AF=0.980263;SB=0;DP4=0,0,34,118 -MN908947.3 29311 . C T 49314 PASS DP=2421;AF=0.989674;SB=0;DP4=2,9,560,1846 -MN908947.3 29587 . G A 29160 PASS DP=798;AF=0.984962;SB=5;DP4=0,1,547,246 diff --git a/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter02.vcf b/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter02.vcf deleted file mode 100644 index c796451..0000000 --- a/benchmark/ERR5409159/ERR5409159.preprocessed.lofreq.vcf.filter02.vcf +++ /dev/null @@ -1,60 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5409159/ERR5409159.preprocessed.lofreq.vcf ERR5409159/ERR5409159.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' ./ERR5409159/ERR5409159.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:31 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 49314 PASS DP=3072;AF=0.98763;SB=0;DP4=1,1,1396,1666 -MN908947.3 913 . C T 49314 PASS DP=3286;AF=0.987827;SB=0;DP4=2,4,1084,2191 -MN908947.3 3037 . C T 49314 PASS DP=2417;AF=0.994621;SB=0;DP4=0,1,995,1418 -MN908947.3 3267 . C T 49314 PASS DP=1566;AF=0.993614;SB=0;DP4=0,0,1009,557 -MN908947.3 5388 . C A 49314 PASS DP=3133;AF=0.991701;SB=0;DP4=0,0,2174,955 -MN908947.3 5986 . C T 49202 PASS DP=1352;AF=0.997041;SB=0;DP4=0,0,988,364 -MN908947.3 6954 . T C 1324 PASS DP=37;AF=1;SB=0;DP4=0,0,13,24 -MN908947.3 8609 . T C 9754 PASS DP=277;AF=0.971119;SB=2;DP4=2,4,59,211 -MN908947.3 11287 . GTCTGGTTTT G 49314 PASS DP=2270;AF=0.988106;SB=13;DP4=85,158,644,1599;INDEL;HRUN=1 -MN908947.3 13297 . C T 49314 PASS DP=4710;AF=0.992144;SB=2;DP4=1,1,1399,3303 -MN908947.3 13763 . G T 49314 PASS DP=2158;AF=0.984245;SB=0;DP4=8,6,1266,873 -MN908947.3 14408 . C T 49314 PASS DP=3189;AF=0.993728;SB=0;DP4=1,1,1559,1626 -MN908947.3 14676 . C T 49314 PASS DP=2035;AF=0.987224;SB=0;DP4=1,0,1373,658 -MN908947.3 15279 . C T 49314 PASS DP=3237;AF=0.991968;SB=0;DP4=2,0,2190,1042 -MN908947.3 16176 . T C 49314 PASS DP=3111;AF=0.992607;SB=0;DP4=1,0,1692,1415 -MN908947.3 17615 . A G 49314 PASS DP=5442;AF=0.991731;SB=0;DP4=1,3,1959,3478 -MN908947.3 21764 . ATACATG A 49314 PASS DP=1461;AF=0.985626;SB=25;DP4=8,15,966,474;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 12904 PASS DP=406;AF=0.832512;SB=14;DP4=11,62,90,248;INDEL;HRUN=3 -MN908947.3 23063 . A T 13330 PASS DP=370;AF=0.991892;SB=0;DP4=0,0,136,234 -MN908947.3 23271 . C A 49314 PASS DP=4448;AF=0.990108;SB=0;DP4=0,0,2825,1620 -MN908947.3 23403 . A G 49314 PASS DP=4117;AF=0.992956;SB=2;DP4=0,2,1427,2688 -MN908947.3 23604 . C A 49314 PASS DP=3999;AF=0.991498;SB=4;DP4=0,1,2511,1485 -MN908947.3 23709 . C T 49314 PASS DP=3425;AF=0.995328;SB=4;DP4=1,0,1101,2321 -MN908947.3 24399 . G A 49314 PASS DP=1954;AF=0.986694;SB=32;DP4=11,5,512,1424 -MN908947.3 24506 . T G 49314 PASS DP=1863;AF=0.987118;SB=0;DP4=2,0,1365,494 -MN908947.3 24914 . G C 49314 PASS DP=5255;AF=0.992579;SB=0;DP4=0,0,1796,3457 -MN908947.3 26730 . G C 49314 PASS DP=5993;AF=0.992491;SB=0;DP4=4,4,2840,3141 -MN908947.3 27972 . C T 49314 PASS DP=3736;AF=0.993308;SB=0;DP4=0,0,1746,1988 -MN908947.3 28048 . G T 49314 PASS DP=2949;AF=0.993557;SB=0;DP4=0,0,1033,1912 -MN908947.3 28111 . A G 49314 PASS DP=2623;AF=0.99085;SB=0;DP4=0,0,1357,1263 -MN908947.3 28270 . TA T 49314 PASS DP=4876;AF=0.849262;SB=179;DP4=517,231,2147,1994;INDEL;HRUN=4 -MN908947.3 28280 . G C 49314 PASS DP=3955;AF=0.995196;SB=0;DP4=0,0,1962,1992 -MN908947.3 28281 . A T 49314 PASS DP=3955;AF=0.994185;SB=0;DP4=0,0,1960,1991 -MN908947.3 28282 . T A 49314 PASS DP=4030;AF=0.996774;SB=0;DP4=0,0,1982,2048 -MN908947.3 28881 . G A 9486 PASS DP=258;AF=1;SB=0;DP4=0,0,113,145 -MN908947.3 28882 . G A 9398 PASS DP=257;AF=0.992218;SB=0;DP4=0,0,112,144 -MN908947.3 28883 . G C 9426 PASS DP=257;AF=0.992218;SB=0;DP4=0,0,112,143 -MN908947.3 28977 . C T 5433 PASS DP=152;AF=0.980263;SB=0;DP4=0,0,34,118 -MN908947.3 29311 . C T 49314 PASS DP=2421;AF=0.989674;SB=0;DP4=2,9,560,1846 -MN908947.3 29587 . G A 29160 PASS DP=798;AF=0.984962;SB=5;DP4=0,1,547,246 diff --git a/benchmark/ERR5409159/ERR5409159.vcf b/benchmark/ERR5409159/ERR5409159.vcf deleted file mode 100644 index c469ae7..0000000 --- a/benchmark/ERR5409159/ERR5409159.vcf +++ /dev/null @@ -1,69 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5409159/ERR5409159.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5409159.vcf; Date=Mon Jun 7 15:58:32 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=135;VDB=0.704481;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,104,20;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 913 . C T 225.417 . DP=120;VDB=0.0518176;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,92,19;MQ=60 GT:PL:AD 1:255,0:0,111 -MN908947.3 3037 . C T 225.417 . DP=123;VDB=0.549544;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,31;MQ=60 GT:PL:AD 1:255,0:0,117 -MN908947.3 3267 . C T 225.417 . DP=97;VDB=0.0093047;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,76,16;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 5388 . C A 225.417 . DP=110;VDB=0.363775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,10;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 5986 . C T 225.417 . DP=90;VDB=0.0485343;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,72,12;MQ=60 GT:PL:AD 1:255,0:0,84 -MN908947.3 6954 . T C 225.417 . DP=24;VDB=0.0691992;SGB=-0.691153;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,10,8;MQ=60 GT:PL:AD 1:255,0:0,18 -MN908947.3 8609 . T C 228.305 . DP=51;VDB=2.59948e-08;SGB=-0.693145;RPB=0.85;MQB=1;MQSB=1;BQB=0.9625;MQ0F=0;AC=1;AN=1;DP4=1,1,24,16;MQ=60 GT:PL:AD 1:255,0:2,40 -MN908947.3 11287 . GTCTGGTTTT G 228.394 . INDEL;IDV=102;IMF=0.944444;DP=108;VDB=0.00631574;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=4,5,81,18;MQ=60 GT:PL:AD 1:255,0:9,99 -MN908947.3 13297 . C T 225.417 . DP=113;VDB=0.00594524;SGB=-0.693147;MQSB=0.998176;MQ0F=0;AC=1;AN=1;DP4=0,0,93,12;MQ=59 GT:PL:AD 1:255,0:0,105 -MN908947.3 13763 . G T 225.417 . DP=129;VDB=0.972602;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,107,17;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 14408 . C T 225.417 . DP=123;VDB=0.210093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,88,24;MQ=60 GT:PL:AD 1:255,0:0,112 -MN908947.3 14676 . C T 225.417 . DP=112;VDB=0.0137719;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,89,17;MQ=60 GT:PL:AD 1:255,0:0,106 -MN908947.3 15279 . C T 225.417 . DP=92;VDB=0.108955;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,12;MQ=60 GT:PL:AD 1:255,0:0,89 -MN908947.3 16176 . T C 225.417 . DP=93;VDB=0.999997;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,77,10;MQ=60 GT:PL:AD 1:255,0:0,87 -MN908947.3 17615 . A G 225.417 . DP=118;VDB=0.16253;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,90,23;MQ=60 GT:PL:AD 1:255,0:0,113 -MN908947.3 21764 . ATACATGT AT 228.41 . INDEL;IDV=80;IMF=0.987654;DP=81;VDB=3.77053e-05;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,62,18;MQ=60 GT:PL:AD 1:255,0:1,80 -MN908947.3 21990 . TTTATTA TTTA 228.326 . INDEL;IDV=37;IMF=0.860465;DP=43;VDB=0.0012936;SGB=-0.693139;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=1,6,25,11;MQ=60 GT:PL:AD 1:255,0:7,36 -MN908947.3 21994 . TTAC T 180.281 . INDEL;IDV=1;IMF=0.025;DP=40;VDB=0.0144848;SGB=-0.693132;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=2,4,24,10;MQ=60 GT:PL:AD 1:207,0:6,34 -MN908947.3 23063 . A T 225.417 . DP=73;VDB=0.512093;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,36,29;MQ=60 GT:PL:AD 1:255,0:0,65 -MN908947.3 23271 . C A 225.417 . DP=126;VDB=0.62606;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,106,15;MQ=60 GT:PL:AD 1:255,0:0,121 -MN908947.3 23403 . A G 225.417 . DP=109;VDB=0.440101;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,96,8;MQ=60 GT:PL:AD 1:255,0:0,104 -MN908947.3 23604 . C A 225.417 . DP=124;VDB=0.0588215;SGB=-0.693147;MQSB=0.998441;MQ0F=0;AC=1;AN=1;DP4=0,0,105,13;MQ=59 GT:PL:AD 1:255,0:0,118 -MN908947.3 23709 . C T 225.417 . DP=112;VDB=0.0814539;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,82,26;MQ=60 GT:PL:AD 1:255,0:0,108 -MN908947.3 24399 . G A 228.372 . DP=94;VDB=9.53254e-05;SGB=-0.693147;RPB=0.0135686;MQB=1;MQSB=1;BQB=0.0414312;MQ0F=0;AC=1;AN=1;DP4=3,0,69,17;MQ=60 GT:PL:AD 1:255,0:3,86 -MN908947.3 24506 . T G 225.417 . DP=99;VDB=0.00738591;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,15;MQ=60 GT:PL:AD 1:255,0:0,94 -MN908947.3 24914 . G C 225.417 . DP=128;VDB=0.670937;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,23;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 26730 . G C 225.417 . DP=128;VDB=0.910743;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,111,13;MQ=60 GT:PL:AD 1:255,0:0,124 -MN908947.3 27972 . C T 225.417 . DP=126;VDB=0.369513;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,100,18;MQ=60 GT:PL:AD 1:255,0:0,118 -MN908947.3 28048 . G T 225.417 . DP=109;VDB=0.0116576;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,86,17;MQ=60 GT:PL:AD 1:255,0:0,103 -MN908947.3 28111 . A G 225.417 . DP=94;VDB=0.898709;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,68,15;MQ=60 GT:PL:AD 1:255,0:0,83 -MN908947.3 28270 . TAAAA TAAA 12.924 . INDEL;IDV=91;IMF=0.81982;DP=111;VDB=0.979327;SGB=-0.693147;MQSB=0.997581;MQ0F=0;AC=1;AN=1;DP4=24,5,70,12;MQ=59 GT:PL:AD 1:99,59:29,82 -MN908947.3 28280 . G C 225.417 . DP=87;VDB=0.0113614;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28281 . A T 225.417 . DP=87;VDB=0.0138443;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28282 . T A 225.417 . DP=88;VDB=0.0151775;SGB=-0.693147;MQSB=0.996067;MQ0F=0;AC=1;AN=1;DP4=0,0,70,16;MQ=59 GT:PL:AD 1:255,0:0,86 -MN908947.3 28881 . G A 225.417 . DP=82;VDB=0.152639;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 28882 . G A 225.417 . DP=81;VDB=0.13136;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,32;MQ=60 GT:PL:AD 1:255,0:0,73 -MN908947.3 28883 . G C 225.417 . DP=81;VDB=0.15109;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,33;MQ=60 GT:PL:AD 1:255,0:0,74 -MN908947.3 28977 . C T 225.417 . DP=46;VDB=0.000220985;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,17,24;MQ=60 GT:PL:AD 1:255,0:0,41 -MN908947.3 29311 . C T 225.417 . DP=85;VDB=2.66274e-09;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,62,18;MQ=60 GT:PL:AD 1:255,0:0,80 -MN908947.3 29587 . G A 228.267 . DP=80;VDB=0.00170351;SGB=-0.693147;RPB=0.847977;MQB=1;MQSB=1;BQB=0.346711;MQ0F=0;AC=1;AN=1;DP4=5,1,52,16;MQ=60 GT:PL:AD 1:255,0:6,68 diff --git a/benchmark/ERR5514762/ERR5514762.annotated.vcf b/benchmark/ERR5514762/ERR5514762.annotated.vcf deleted file mode 100644 index ab0df01..0000000 --- a/benchmark/ERR5514762/ERR5514762.annotated.vcf +++ /dev/null @@ -1,68 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5514762/ERR5514762.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5514762.vcf; Date=Mon Jun 7 16:02:45 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 16:03:04 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5514762.normalized.vcf -; Date=Mon Jun 7 16:03:04 2021 -##bcftools/csqVersion=1.12+htslib-1.12 -##bcftools/csqCommand=csq --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --gff-annot /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.101.gff3 -o ERR5514762.annotated.vcf /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5514762/ERR5514762.normalized.vcf; Date=Mon Jun 7 16:03:05 2021 -##INFO= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=49;VDB=0.908417;SGB=-0.693143;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,28,10;MQ=60 GT:PL:AD 1:255,0:0,38 -MN908947.3 913 . C T 228.31 . DP=31;VDB=0.0238607;SGB=-0.693054;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,22,6;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|216S|913C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|216S|913C>T GT:PL:AD:BCSQ 1:255,0:1,28:5 -MN908947.3 2453 . C T 228.392 . DP=58;VDB=0.368441;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,31,19;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|730L>730F|2453C>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|730L>730F|2453C>T GT:PL:AD:BCSQ 1:255,0:1,50:5 -MN908947.3 3037 . C T 225.417 . DP=58;VDB=0.285883;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,16;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|924F|3037C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|924F|3037C>T GT:PL:AD:BCSQ 1:255,0:0,48:5 -MN908947.3 5087 . A G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1608K>1608E|5087A>G,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1608K>1608E|5087A>G GT:PL:AD:BCSQ 1:37,0:0,1:5 -MN908947.3 5388 . C A 225.417 . DP=103;VDB=0.125998;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,97,3;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|1708A>1708D|5388C>A,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|1708A>1708D|5388C>A GT:PL:AD:BCSQ 1:255,0:0,100:5 -MN908947.3 5986 . C T 225.417 . DP=34;VDB=0.389335;SGB=-0.693054;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,24,4;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000003|protein_coding|+|1907F|5986C>T,synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|1907F|5986C>T GT:PL:AD:BCSQ 1:255,0:0,28:5 -MN908947.3 7414 . G T 4.38466 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=32;BCSQ=missense|ORF1ab|ENSSAST00005000003|protein_coding|+|2383M>2383I|7414G>T,missense|ORF1ab|ENSSAST00005000002|protein_coding|+|2383M>2383I|7414G>T GT:PL:AD:BCSQ 1:32,0:0,1:5 -MN908947.3 14408 . C T 225.417 . DP=80;VDB=0.0239241;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,44,26;MQ=60;BCSQ=synonymous|ORF1ab|ENSSAST00005000002|protein_coding|+|4715L|14408C>T GT:PL:AD:BCSQ 1:255,0:0,70:1 -MN908947.3 15279 . C T 228.38 . DP=53;VDB=0.565758;SGB=-0.693145;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,34,6;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5005T>5005I|15279C>T GT:PL:AD:BCSQ 1:255,0:1,40:1 -MN908947.3 16176 . T C 225.417 . DP=48;VDB=0.00966111;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,7;MQ=60;BCSQ=missense|ORF1ab|ENSSAST00005000002|protein_coding|+|5304L>5304P|16176T>C GT:PL:AD:BCSQ 1:255,0:0,45:1 -MN908947.3 21764 . ATACATG A 228.332 . INDEL;IDV=58;IMF=0.95082;DP=61;VDB=0.0190795;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=3,1,43,14;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|68IHV>68I|21764ATACATG>A GT:PL:AD:BCSQ 1:255,0:4,57:1 -MN908947.3 21990 . TTTA T 192.24 . INDEL;IDV=26;IMF=0.787879;DP=33;VDB=2.8013e-06;SGB=-0.692914;MQSB=0.978183;MQ0F=0;AC=1;AN=1;DP4=4,4,18,7;MQ=58;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA;BCSQ=inframe_deletion|S|ENSSAST00005000004|protein_coding|+|143VY>141V|21990TTTA>T GT:PL:AD:BCSQ 1:255,36:8,25:1 -MN908947.3 23063 . A T 225.417 . DP=104;VDB=0.759419;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,23;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|501N>498Y|23063A>T GT:PL:AD:BCSQ 1:255,0:0,102:1 -MN908947.3 23271 . C A 115.139 . DP=8;VDB=0.250121;SGB=-0.616816;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,5,1;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|570A>567D|23271C>A GT:PL:AD:BCSQ 1:154,12:1,6:1 -MN908947.3 23403 . A G 198.421 . DP=10;VDB=0.326789;SGB=-0.636426;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,5,2;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|614D>611G|23403A>G GT:PL:AD:BCSQ 1:228,0:0,6:1 -MN908947.3 23604 . C A 225.417 . DP=94;VDB=0.13874;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,19;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|681P>678H|23604C>A GT:PL:AD:BCSQ 1:255,0:0,92:1 -MN908947.3 23709 . C T 225.417 . DP=83;VDB=0.0336649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,23;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|716T>713I|23709C>T GT:PL:AD:BCSQ 1:255,0:0,78:1 -MN908947.3 24506 . T G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|982S>979A|24506T>G GT:PL:AD:BCSQ 1:37,0:0,1:1 -MN908947.3 24914 . G C 225.422 . DP=107;VDB=0.189845;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,8;MQ=60;BCSQ=missense|S|ENSSAST00005000004|protein_coding|+|1118D>1115H|24914G>C GT:PL:AD:BCSQ 1:255,0:0,102:1 -MN908947.3 27972 . C T 225.417 . DP=72;VDB=0.514775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,20;MQ=60;BCSQ=stop_gained|ORF8|ENSSAST00005000008|protein_coding|+|27Q>27*|27972C>T GT:PL:AD:BCSQ 1:255,0:0,61:1 -MN908947.3 28048 . G T 225.417 . DP=65;VDB=0.262381;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,19;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|52R>52I|28048G>T GT:PL:AD:BCSQ 1:255,0:0,57:1 -MN908947.3 28111 . A G 225.417 . DP=48;VDB=0.288894;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,10;MQ=60;BCSQ=*missense|ORF8|ENSSAST00005000008|protein_coding|+|73Y>73C|28111A>G GT:PL:AD:BCSQ 1:255,0:0,41:1 -MN908947.3 28280 . G C 228.319 . DP=42;VDB=0.00821796;SGB=-0.693141;RPB=0.27027;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|3D>3L|28280G>C+28281A>T+28282T>A GT:PL:AD:BCSQ 1:255,0:2,37:1 -MN908947.3 28281 . A T 228.292 . DP=42;VDB=0.00728612;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:2,37:1 -MN908947.3 28282 . T A 228.296 . DP=43;VDB=0.00647971;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=1;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59;BCSQ=@28280 GT:PL:AD:BCSQ 1:255,0:2,37:1 -MN908947.3 28677 . C T 228.405 . DP=99;VDB=0.432583;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,87,7;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|135T>135I|28677C>T GT:PL:AD:BCSQ 1:255,0:1,94:1 -MN908947.3 28881 . G A 9.88514 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|203R>203K|28881G>A+28882G>A GT:PL:AD:BCSQ 1:39,0:0,1:1 -MN908947.3 28882 . G A 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60;BCSQ=@28881 GT:PL:AD:BCSQ 1:38,0:0,1:1 -MN908947.3 28883 . G C 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|204G>204R|28883G>C GT:PL:AD:BCSQ 1:38,0:0,1:1 -MN908947.3 28977 . C T 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60;BCSQ=missense|N|ENSSAST00005000005|protein_coding|+|235S>235F|28977C>T GT:PL:AD:BCSQ 1:38,0:0,1:1 diff --git a/benchmark/ERR5514762/ERR5514762.normalized.vcf b/benchmark/ERR5514762/ERR5514762.normalized.vcf deleted file mode 100644 index a289aa5..0000000 --- a/benchmark/ERR5514762/ERR5514762.normalized.vcf +++ /dev/null @@ -1,64 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5514762/ERR5514762.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5514762.vcf; Date=Mon Jun 7 16:02:45 2021 -##INFO= -##bcftools_normVersion=1.12+htslib-1.12 -##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Mon Jun 7 16:03:04 2021 -##FORMAT= -##bcftools_normCommand=norm --rm-dup exact -o ERR5514762.normalized.vcf -; Date=Mon Jun 7 16:03:04 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=49;VDB=0.908417;SGB=-0.693143;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,28,10;MQ=60 GT:PL:AD 1:255,0:0,38 -MN908947.3 913 . C T 228.31 . DP=31;VDB=0.0238607;SGB=-0.693054;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,22,6;MQ=60 GT:PL:AD 1:255,0:1,28 -MN908947.3 2453 . C T 228.392 . DP=58;VDB=0.368441;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,31,19;MQ=60 GT:PL:AD 1:255,0:1,50 -MN908947.3 3037 . C T 225.417 . DP=58;VDB=0.285883;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,16;MQ=60 GT:PL:AD 1:255,0:0,48 -MN908947.3 5087 . A G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60 GT:PL:AD 1:37,0:0,1 -MN908947.3 5388 . C A 225.417 . DP=103;VDB=0.125998;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,97,3;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 5986 . C T 225.417 . DP=34;VDB=0.389335;SGB=-0.693054;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,24,4;MQ=60 GT:PL:AD 1:255,0:0,28 -MN908947.3 7414 . G T 4.38466 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=32 GT:PL:AD 1:32,0:0,1 -MN908947.3 14408 . C T 225.417 . DP=80;VDB=0.0239241;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,44,26;MQ=60 GT:PL:AD 1:255,0:0,70 -MN908947.3 15279 . C T 228.38 . DP=53;VDB=0.565758;SGB=-0.693145;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,34,6;MQ=60 GT:PL:AD 1:255,0:1,40 -MN908947.3 16176 . T C 225.417 . DP=48;VDB=0.00966111;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,7;MQ=60 GT:PL:AD 1:255,0:0,45 -MN908947.3 21764 . ATACATG A 228.332 . INDEL;IDV=58;IMF=0.95082;DP=61;VDB=0.0190795;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=3,1,43,14;MQ=60;OLD_CLUMPED=MN908947.3|21764|ATACATGT|AT GT:PL:AD 1:255,0:4,57 -MN908947.3 21990 . TTTA T 192.24 . INDEL;IDV=26;IMF=0.787879;DP=33;VDB=2.8013e-06;SGB=-0.692914;MQSB=0.978183;MQ0F=0;AC=1;AN=1;DP4=4,4,18,7;MQ=58;OLD_CLUMPED=MN908947.3|21990|TTTATTA|TTTA GT:PL:AD 1:255,36:8,25 -MN908947.3 23063 . A T 225.417 . DP=104;VDB=0.759419;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,23;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 23271 . C A 115.139 . DP=8;VDB=0.250121;SGB=-0.616816;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,5,1;MQ=60 GT:PL:AD 1:154,12:1,6 -MN908947.3 23403 . A G 198.421 . DP=10;VDB=0.326789;SGB=-0.636426;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,5,2;MQ=60 GT:PL:AD 1:228,0:0,6 -MN908947.3 23604 . C A 225.417 . DP=94;VDB=0.13874;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,19;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 23709 . C T 225.417 . DP=83;VDB=0.0336649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,23;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 24506 . T G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60 GT:PL:AD 1:37,0:0,1 -MN908947.3 24914 . G C 225.422 . DP=107;VDB=0.189845;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,8;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 27972 . C T 225.417 . DP=72;VDB=0.514775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,20;MQ=60 GT:PL:AD 1:255,0:0,61 -MN908947.3 28048 . G T 225.417 . DP=65;VDB=0.262381;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,19;MQ=60 GT:PL:AD 1:255,0:0,57 -MN908947.3 28111 . A G 225.417 . DP=48;VDB=0.288894;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,10;MQ=60 GT:PL:AD 1:255,0:0,41 -MN908947.3 28280 . G C 228.319 . DP=42;VDB=0.00821796;SGB=-0.693141;RPB=0.27027;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28281 . A T 228.292 . DP=42;VDB=0.00728612;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28282 . T A 228.296 . DP=43;VDB=0.00647971;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=1;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28677 . C T 228.405 . DP=99;VDB=0.432583;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,87,7;MQ=60 GT:PL:AD 1:255,0:1,94 -MN908947.3 28881 . G A 9.88514 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:39,0:0,1 -MN908947.3 28882 . G A 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 -MN908947.3 28883 . G C 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 -MN908947.3 28977 . C T 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 diff --git a/benchmark/ERR5514762/ERR5514762.preprocessed.gatk.vcf b/benchmark/ERR5514762/ERR5514762.preprocessed.gatk.vcf deleted file mode 100644 index 11a1c14..0000000 --- a/benchmark/ERR5514762/ERR5514762.preprocessed.gatk.vcf +++ /dev/null @@ -1,54 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##source=HaplotypeCaller -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 3783.04 . AC=1;AF=1.00;AN=1;DP=151;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.09;SOR=0.764 GT:AD:DP:GQ:PL 1:0,145:145:99:3793,0 -MN908947.3 913 . C T 1809.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.798;DP=76;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=24.45;ReadPosRankSum=1.910;SOR=0.548 GT:AD:DP:GQ:PL 1:3,71:74:99:1819,0 -MN908947.3 2453 . C T 4663.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.510;DP=175;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.65;ReadPosRankSum=-1.321;SOR=1.052 GT:AD:DP:GQ:PL 1:2,173:175:99:4673,0 -MN908947.3 3037 . C T 6693.04 . AC=1;AF=1.00;AN=1;DP=234;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=28.97;SOR=0.911 GT:AD:DP:GQ:PL 1:0,231:231:99:6703,0 -MN908947.3 5259 . C CAGGCACAGG 254.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.616;DP=22;FS=10.792;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=15.88;ReadPosRankSum=-3.146;SOR=4.407 GT:AD:DP:GQ:PL 1:5,11:16:99:264,0 -MN908947.3 5388 . C A 91259.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-2.302;DP=2871;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=32.16;ReadPosRankSum=-0.752;SOR=0.088 GT:AD:DP:GQ:PL 1:4,2834:2838:99:91269,0 -MN908947.3 5986 . C T 2218.04 . AC=1;AF=1.00;AN=1;DP=74;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.81;SOR=1.577 GT:AD:DP:GQ:PL 1:0,72:72:99:2228,0 -MN908947.3 14408 . C T 31884.04 . AC=1;AF=1.00;AN=1;DP=1141;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.06;SOR=0.751 GT:AD:DP:GQ:PL 1:0,1097:1097:99:31894,0 -MN908947.3 15279 . C T 5126.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-1.945;DP=214;FS=1.607;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=24.29;ReadPosRankSum=-0.485;SOR=0.406 GT:AD:DP:GQ:PL 1:6,205:211:99:5136,0 -MN908947.3 16176 . T C 38186.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.763;DP=1256;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.25;ReadPosRankSum=0.940;SOR=0.793 GT:AD:DP:GQ:PL 1:2,1220:1222:99:38196,0 -MN908947.3 21574 . T A 35.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.000;DP=3;FS=4.771;MLEAC=1;MLEAF=1.00;MQ=50.64;MQRankSum=-0.967;QD=11.68;ReadPosRankSum=-0.967;SOR=2.225 GT:AD:DP:GQ:PL 1:1,2:3:45:45,0 -MN908947.3 21764 . ATACATG A 23818.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.474;DP=616;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.26;MQRankSum=0.239;QD=25.75;ReadPosRankSum=2.314;SOR=0.983 GT:AD:DP:GQ:PL 1:2,537:539:99:23828,0 -MN908947.3 21990 . TTTA T 5176.01 . AC=1;AF=1.00;AN=1;DP=127;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.81;QD=28.44;SOR=1.510 GT:AD:DP:GQ:PL 1:0,116:116:99:5186,0 -MN908947.3 23063 . A T 62329.04 . AC=1;AF=1.00;AN=1;DP=2110;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.75;SOR=1.200 GT:AD:DP:GQ:PL 1:0,2095:2095:99:62339,0 -MN908947.3 23271 . C A 182.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=0.792;DP=7;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.01;ReadPosRankSum=0.792;SOR=1.179 GT:AD:DP:GQ:PL 1:1,6:7:99:192,0 -MN908947.3 23403 . A G 310.04 . AC=1;AF=1.00;AN=1;DP=13;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=25.84;SOR=1.445 GT:AD:DP:GQ:PL 1:0,12:12:99:320,0 -MN908947.3 23604 . C A 52306.04 . AC=1;AF=1.00;AN=1;DP=1812;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.16;SOR=0.920 GT:AD:DP:GQ:PL 1:0,1794:1794:99:52316,0 -MN908947.3 23709 . C T 50865.04 . AC=1;AF=1.00;AN=1;DP=1766;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=29.37;SOR=1.492 GT:AD:DP:GQ:PL 1:0,1732:1732:99:50875,0 -MN908947.3 24914 . G C 154814.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.253;DP=4857;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.06;ReadPosRankSum=0.687;SOR=1.324 GT:AD:DP:GQ:PL 1:2,4681:4683:99:154824,0 -MN908947.3 27972 . C T 8018.04 . AC=1;AF=1.00;AN=1;DP=307;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=27.37;SOR=0.771 GT:AD:DP:GQ:PL 1:0,293:293:99:8028,0 -MN908947.3 28048 . G T 7653.04 . AC=1;AF=1.00;AN=1;DP=284;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.95;SOR=0.943 GT:AD:DP:GQ:PL 1:0,284:284:99:7663,0 -MN908947.3 28111 . A G 6377.04 . AC=1;AF=1.00;AN=1;DP=256;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=26.46;SOR=0.752 GT:AD:DP:GQ:PL 1:0,241:241:99:6387,0 -MN908947.3 28270 . TA T 25337.01 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.218;DP=593;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.94;MQRankSum=-0.011;QD=25.68;ReadPosRankSum=0.489;SOR=0.835 GT:AD:DP:GQ:PL 1:2,570:572:99:25347,0 -MN908947.3 28280 . G C 26733.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.076;DP=613;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.91;MQRankSum=-0.064;QD=27.92;ReadPosRankSum=1.913;SOR=0.792 GT:AD:DP:GQ:PL 1:2,611:613:99:26743,0 -MN908947.3 28281 . A T 26699.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.053;DP=648;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.91;MQRankSum=-0.064;QD=30.16;ReadPosRankSum=2.011;SOR=0.789 GT:AD:DP:GQ:PL 1:2,610:612:99:26709,0 -MN908947.3 28282 . T A 26700.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.024;DP=691;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.91;MQRankSum=-0.064;QD=28.70;ReadPosRankSum=1.684;SOR=0.789 GT:AD:DP:GQ:PL 1:2,610:612:99:26710,0 -MN908947.3 28677 . C T 123065.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=1.185;DP=3786;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=33.17;ReadPosRankSum=-1.309;SOR=0.583 GT:AD:DP:GQ:PL 1:6,3704:3710:99:123075,0 -MN908947.3 29737 . G C 116.04 . AC=1;AF=1.00;AN=1;BaseQRankSum=2.519;DP=24;FS=24.644;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=4.84;ReadPosRankSum=-0.669;SOR=5.282 GT:AD:DP:GQ:PL 1:11,13:24:99:126,0 diff --git a/benchmark/ERR5514762/ERR5514762.preprocessed.ivar.tsv b/benchmark/ERR5514762/ERR5514762.preprocessed.ivar.tsv deleted file mode 100644 index dd5183e..0000000 --- a/benchmark/ERR5514762/ERR5514762.preprocessed.ivar.tsv +++ /dev/null @@ -1,111 +0,0 @@ -REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA -MN908947.3 37 C G 5 2 44 1 0 29 0.166667 6 0.5 FALSE NA NA NA NA NA -MN908947.3 38 A G 12 4 44 1 0 33 0.0769231 13 0.448276 FALSE NA NA NA NA NA -MN908947.3 241 C T 0 0 0 84 9 63 1 84 3.19406e-65 TRUE NA NA NA NA NA -MN908947.3 330 A G 234 44 48 13 0 32 0.0526316 247 1.47599e-05 TRUE CDS:ENSSASP00005000003 CAG Q CGG R -MN908947.3 330 A G 234 44 48 13 0 32 0.0526316 247 1.47599e-05 TRUE CDS:ENSSASP00005000002 CAG Q CGG R -MN908947.3 739 A G 26 0 67 1 0 33 0.037037 27 0.369863 FALSE CDS:ENSSASP00005000003 CAA Q CAG Q -MN908947.3 739 A G 26 0 67 1 0 33 0.037037 27 0.369863 FALSE CDS:ENSSASP00005000002 CAA Q CAG Q -MN908947.3 913 C T 2 1 52 40 9 67 0.952381 42 3.90369e-29 TRUE CDS:ENSSASP00005000003 TCC S TCT S -MN908947.3 913 C T 2 1 52 40 9 67 0.952381 42 3.90369e-29 TRUE CDS:ENSSASP00005000002 TCC S TCT S -MN908947.3 2218 T C 10 0 63 1 0 20 0.0909091 11 0.37931 FALSE CDS:ENSSASP00005000003 TTT F TTC F -MN908947.3 2218 T C 10 0 63 1 0 20 0.0909091 11 0.37931 FALSE CDS:ENSSASP00005000002 TTT F TTC F -MN908947.3 2453 C T 1 0 71 101 27 64 0.990196 102 1.56863e-76 TRUE CDS:ENSSASP00005000003 CTC L TTC F -MN908947.3 2453 C T 1 0 71 101 27 64 0.990196 102 1.56863e-76 TRUE CDS:ENSSASP00005000002 CTC L TTC F -MN908947.3 3037 C T 0 0 0 143 39 61 1 143 3.4288e-107 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 3037 C T 0 0 0 143 39 61 1 143 3.4288e-107 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 3621 G A 15 0 71 1 0 75 0.0625 16 0.347826 FALSE CDS:ENSSASP00005000003 GGC G GAC D -MN908947.3 3621 G A 15 0 71 1 0 75 0.0625 16 0.347826 FALSE CDS:ENSSASP00005000002 GGC G GAC D -MN908947.3 5087 A G 0 0 0 1 0 37 1 1 1 FALSE CDS:ENSSASP00005000003 AAA K GAA E -MN908947.3 5087 A G 0 0 0 1 0 37 1 1 1 FALSE CDS:ENSSASP00005000002 AAA K GAA E -MN908947.3 5260 T A 3 1 55 2 0 72 0.4 5 0.128205 FALSE CDS:ENSSASP00005000003 ACT T ACA T -MN908947.3 5260 T A 3 1 55 2 0 72 0.4 5 0.128205 FALSE CDS:ENSSASP00005000002 ACT T ACA T -MN908947.3 5388 C A 4 0 38 2391 3 60 0.997497 2397 0 TRUE CDS:ENSSASP00005000003 GCT A GAT D -MN908947.3 5388 C A 4 0 38 2391 3 60 0.997497 2397 0 TRUE CDS:ENSSASP00005000002 GCT A GAT D -MN908947.3 5807 A G 17 3 64 1 0 77 0.0555556 18 0.36 FALSE CDS:ENSSASP00005000003 ATA I GTA V -MN908947.3 5807 A G 17 3 64 1 0 77 0.0555556 18 0.36 FALSE CDS:ENSSASP00005000002 ATA I GTA V -MN908947.3 5986 C T 0 0 0 49 0 57 1 49 2.7535e-35 TRUE CDS:ENSSASP00005000003 TTC F TTT F -MN908947.3 5986 C T 0 0 0 49 0 57 1 49 2.7535e-35 TRUE CDS:ENSSASP00005000002 TTC F TTT F -MN908947.3 6340 T C 8 2 56 1 0 70 0.111111 9 0.409091 FALSE CDS:ENSSASP00005000003 TTT F TTC F -MN908947.3 6340 T C 8 2 56 1 0 70 0.111111 9 0.409091 FALSE CDS:ENSSASP00005000002 TTT F TTC F -MN908947.3 6380 C G 12 3 61 2 2 39 0.142857 14 0.144444 FALSE CDS:ENSSASP00005000003 CTT L GTT V -MN908947.3 6380 C G 12 3 61 2 2 39 0.142857 14 0.144444 FALSE CDS:ENSSASP00005000002 CTT L GTT V -MN908947.3 6410 G T 26 7 65 1 1 31 0.037037 27 0.375 FALSE CDS:ENSSASP00005000003 GAA E TAA * -MN908947.3 6410 G T 26 7 65 1 1 31 0.037037 27 0.375 FALSE CDS:ENSSASP00005000002 GAA E TAA * -MN908947.3 6418 A C 25 6 67 1 1 32 0.0384615 26 0.366197 FALSE CDS:ENSSASP00005000003 GTA V GTC V -MN908947.3 6418 A C 25 6 67 1 1 32 0.0384615 26 0.366197 FALSE CDS:ENSSASP00005000002 GTA V GTC V -MN908947.3 6425 A T 23 6 70 1 1 33 0.0416667 24 0.363636 FALSE CDS:ENSSASP00005000003 AAT N TAT Y -MN908947.3 6425 A T 23 6 70 1 1 33 0.0416667 24 0.363636 FALSE CDS:ENSSASP00005000002 AAT N TAT Y -MN908947.3 6435 T A 18 4 70 1 0 71 0.0526316 19 0.339286 FALSE CDS:ENSSASP00005000003 ATA I AAA K -MN908947.3 6435 T A 18 4 70 1 0 71 0.0526316 19 0.339286 FALSE CDS:ENSSASP00005000002 ATA I AAA K -MN908947.3 6696 C +T 291 57 63 21 0 20 0.0427699 491 3.49844e-06 TRUE NA NA NA NA NA -MN908947.3 7414 G T 1 0 37 1 0 33 0.5 2 0.666667 FALSE CDS:ENSSASP00005000003 ATG M ATT I -MN908947.3 7414 G T 1 0 37 1 0 33 0.5 2 0.666667 FALSE CDS:ENSSASP00005000002 ATG M ATT I -MN908947.3 7460 C A 2 0 55 1 0 38 0.333333 3 0.428571 FALSE CDS:ENSSASP00005000003 CAT H AAT N -MN908947.3 7460 C A 2 0 55 1 0 38 0.333333 3 0.428571 FALSE CDS:ENSSASP00005000002 CAT H AAT N -MN908947.3 7473 G A 3 0 47 1 0 33 0.25 4 0.5 FALSE CDS:ENSSASP00005000003 GGT G GAT D -MN908947.3 7473 G A 3 0 47 1 0 33 0.25 4 0.5 FALSE CDS:ENSSASP00005000002 GGT G GAT D -MN908947.3 7635 C A 18 1 50 1 0 73 0.0526316 19 0.413043 FALSE CDS:ENSSASP00005000003 ACA T AAA K -MN908947.3 7635 C A 18 1 50 1 0 73 0.0526316 19 0.413043 FALSE CDS:ENSSASP00005000002 ACA T AAA K -MN908947.3 8888 C T 0 0 0 1 1 39 1 1 0.5 FALSE CDS:ENSSASP00005000003 CGC R TGC C -MN908947.3 8888 C T 0 0 0 1 1 39 1 1 0.5 FALSE CDS:ENSSASP00005000002 CGC R TGC C -MN908947.3 10516 T C 6 0 50 1 0 32 0.142857 7 0.411765 FALSE CDS:ENSSASP00005000003 TAT Y TAC Y -MN908947.3 10516 T C 6 0 50 1 0 32 0.142857 7 0.411765 FALSE CDS:ENSSASP00005000002 TAT Y TAC Y -MN908947.3 10563 G T 7 1 51 1 0 35 0.125 8 0.4 FALSE CDS:ENSSASP00005000003 GGA G GTA V -MN908947.3 10563 G T 7 1 51 1 0 35 0.125 8 0.4 FALSE CDS:ENSSASP00005000002 GGA G GTA V -MN908947.3 11694 T C 3 0 36 1 0 39 0.2 5 0.444444 FALSE CDS:ENSSASP00005000003 GTT V GCT A -MN908947.3 11694 T C 3 0 36 1 0 39 0.2 5 0.444444 FALSE CDS:ENSSASP00005000002 GTT V GCT A -MN908947.3 11694 T A 3 0 36 1 0 39 0.2 5 0.444444 FALSE CDS:ENSSASP00005000003 GTT V GAT D -MN908947.3 11694 T A 3 0 36 1 0 39 0.2 5 0.444444 FALSE CDS:ENSSASP00005000002 GTT V GAT D -MN908947.3 12332 G A 5 3 53 1 0 78 0.166667 6 0.428571 FALSE CDS:ENSSASP00005000003 GCA A ACA T -MN908947.3 12332 G A 5 3 53 1 0 78 0.166667 6 0.428571 FALSE CDS:ENSSASP00005000002 GCA A ACA T -MN908947.3 12870 C G 30 2 67 1 0 21 0.0322581 31 0.356322 FALSE CDS:ENSSASP00005000003 ACT T AGT S -MN908947.3 12870 C G 30 2 67 1 0 21 0.0322581 31 0.356322 FALSE CDS:ENSSASP00005000002 ACT T AGT S -MN908947.3 12967 A G 17 3 70 2 0 34 0.105263 19 0.124093 FALSE CDS:ENSSASP00005000003 TTA L TTG L -MN908947.3 12967 A G 17 3 70 2 0 34 0.105263 19 0.124093 FALSE CDS:ENSSASP00005000002 TTA L TTG L -MN908947.3 14408 C T 0 0 0 686 127 63 1 686 0 TRUE CDS:ENSSASP00005000002 CTA L TTA L -MN908947.3 15279 C T 4 0 57 114 0 68 0.966102 118 2.98135e-85 TRUE CDS:ENSSASP00005000002 ACC T ATC I -MN908947.3 16105 A G 31 10 64 1 1 33 0.03125 32 0.380952 FALSE CDS:ENSSASP00005000002 TAA * TAG * -MN908947.3 16176 T C 2 1 37 1097 4 58 0.99818 1099 0 TRUE CDS:ENSSASP00005000002 CTT L CCT P -MN908947.3 16753 A T 1 0 38 1 1 37 0.5 2 0.666667 FALSE CDS:ENSSASP00005000002 CTA L CTT L -MN908947.3 17975 A G 14 0 62 1 0 32 0.0666667 15 0.365854 FALSE CDS:ENSSASP00005000002 ACC T GCC A -MN908947.3 18974 T G 14 2 57 3 2 38 0.176471 17 0.0592334 FALSE CDS:ENSSASP00005000002 TTC F GTC V -MN908947.3 20153 A -N 50 34 50 2 0 20 0.030303 66 0.195402 FALSE NA NA NA NA NA -MN908947.3 20214 A G 6 2 58 1 1 33 0.142857 7 0.411765 FALSE CDS:ENSSASP00005000002 GAA E GGA G -MN908947.3 20245 A T 0 0 0 1 0 72 1 1 0.5 FALSE CDS:ENSSASP00005000002 AAA K AAT N -MN908947.3 20578 G T 281 1 56 11 0 56 0.0376712 292 3.97346e-05 TRUE CDS:ENSSASP00005000002 AAG K AAT N -MN908947.3 21075 T A 0 0 0 2 2 39 1 2 0.333333 FALSE CDS:ENSSASP00005000002 TTA L TAA * -MN908947.3 21764 A -NNNNNN 316 2 66 530 0 20 0.953237 556 8.63155e-151 TRUE NA NA NA NA NA -MN908947.3 21990 T -NNN 80 30 60 105 0 20 0.807692 130 9.2463e-31 TRUE NA NA NA NA NA -MN908947.3 21994 T C 64 24 60 4 3 34 0.0588235 68 0.0210812 FALSE CDS:ENSSASP00005000004 TAT Y TAC Y -MN908947.3 23063 A T 0 0 0 1380 432 64 1 1380 0 TRUE CDS:ENSSASP00005000004 AAT N TAT Y -MN908947.3 23271 C A 1 0 62 5 0 45 0.833333 6 0.002997 TRUE CDS:ENSSASP00005000004 GCT A GAT D -MN908947.3 23403 A G 0 0 0 8 4 52 1 8 7.9384e-06 TRUE CDS:ENSSASP00005000004 GAT D GGT G -MN908947.3 23604 C A 0 0 0 1519 47 63 1 1519 0 TRUE CDS:ENSSASP00005000004 CCT P CAT H -MN908947.3 23709 C T 0 0 0 1213 493 57 0.999176 1214 0 TRUE CDS:ENSSASP00005000004 ACA T ATA I -MN908947.3 24506 T G 0 0 0 1 0 75 1 1 0.5 FALSE CDS:ENSSASP00005000004 TCA S GCA A -MN908947.3 24626 G A 0 0 0 1 1 31 1 1 1 FALSE CDS:ENSSASP00005000004 GCT A ACT T -MN908947.3 24686 T G 0 0 0 1 1 29 1 1 1 FALSE CDS:ENSSASP00005000004 TTT F GTT V -MN908947.3 24703 T G 5 0 64 1 0 34 0.125 8 0.315789 FALSE CDS:ENSSASP00005000004 TAT Y TAG * -MN908947.3 24703 T A 5 0 64 2 0 49 0.25 8 0.110526 FALSE CDS:ENSSASP00005000004 TAT Y TAA * -MN908947.3 24914 G C 1 0 78 4488 1726 59 0.999777 4489 0 TRUE CDS:ENSSASP00005000004 GAC D CAC H -MN908947.3 26467 G C 2 1 56 15 1 70 0.882353 17 1.24399e-10 TRUE CDS:ENSSASP00005000010 GTC V CTC L -MN908947.3 27972 C T 0 0 0 169 28 65 1 169 7.12284e-131 TRUE CDS:ENSSASP00005000008 CAA Q TAA * -MN908947.3 28048 G T 0 0 0 158 31 68 1 158 4.82139e-125 TRUE CDS:ENSSASP00005000008 AGA R ATA I -MN908947.3 28111 A G 0 0 0 137 19 64 1 137 4.78776e-107 TRUE CDS:ENSSASP00005000008 TAC Y TGC C -MN908947.3 28253 C -N 157 64 53 60 0 20 0.269058 223 2.38554e-18 TRUE NA NA NA NA NA -MN908947.3 28254 A C 101 8 60 78 13 54 0.435754 179 6.27387e-43 TRUE CDS:ENSSASP00005000008 ATC I CTC L -MN908947.3 28270 T -N 1360 104 62 2183 0 20 0.974989 2239 0 TRUE NA NA NA NA NA -MN908947.3 28280 G C 4 1 56 1373 106 63 0.997095 1377 0 TRUE CDS:ENSSASP00005000005 GAT D CAT H -MN908947.3 28281 A T 4 1 61 1373 107 63 0.997095 1377 0 TRUE CDS:ENSSASP00005000005 GAT D GTT V -MN908947.3 28282 T A 3 1 58 1431 119 63 0.997213 1435 0 TRUE CDS:ENSSASP00005000005 GAT D GAA E -MN908947.3 28677 C T 4 2 51 3959 1808 58 0.998991 3963 0 TRUE CDS:ENSSASP00005000005 ACT T ATT I -MN908947.3 28773 T C 4 3 36 1 1 34 0.2 5 0.555556 FALSE CDS:ENSSASP00005000005 TTG L TCG S -MN908947.3 28881 G A 0 0 0 1 1 39 1 1 1 FALSE CDS:ENSSASP00005000005 AGG R AAG K -MN908947.3 28882 G A 0 0 0 1 1 38 1 1 1 FALSE CDS:ENSSASP00005000005 AGG R AGA R -MN908947.3 28883 G C 0 0 0 1 1 38 1 1 1 FALSE CDS:ENSSASP00005000005 GGA G CGA R -MN908947.3 28977 C T 0 0 0 1 1 38 1 1 1 FALSE CDS:ENSSASP00005000005 TCT S TTT F -MN908947.3 29577 T A 37 2 54 5 0 71 0.119048 42 0.00695038 TRUE CDS:ENSSASP00005000013 TTC F TAC Y -MN908947.3 29736 G C 18 1 44 1 0 74 0.0526316 19 0.44186 FALSE NA NA NA NA NA -MN908947.3 29737 G C 6 1 68 11 0 35 0.647059 17 3.91712e-06 TRUE NA NA NA NA NA -MN908947.3 29743 C A 6 1 68 1 0 27 0.142857 7 0.388889 FALSE NA NA NA NA NA diff --git a/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter01.vcf b/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter01.vcf deleted file mode 100644 index fcb3cd8..0000000 --- a/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter01.vcf +++ /dev/null @@ -1,48 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5514762/ERR5514762.preprocessed.lofreq.vcf ERR5514762/ERR5514762.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.1' ./ERR5514762/ERR5514762.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:18 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 4980 PASS DP=143;AF=0.965035;SB=0;DP4=0,0,72,71 -MN908947.3 913 . C T 2623 PASS DP=74;AF=0.945946;SB=0;DP4=1,2,31,40 -MN908947.3 2453 . C T 6346 PASS DP=177;AF=0.966102;SB=0;DP4=1,1,74,101 -MN908947.3 3037 . C T 8470 PASS DP=229;AF=0.9869;SB=0;DP4=0,0,102,127 -MN908947.3 5388 . C A 49314 PASS DP=3827;AF=0.977267;SB=2;DP4=2,0,2409,1410 -MN908947.3 5986 . C T 2665 PASS DP=74;AF=0.986486;SB=0;DP4=0,0,49,25 -MN908947.3 14408 . C T 42303 PASS DP=1143;AF=0.988626;SB=0;DP4=0,0,562,580 -MN908947.3 15279 . C T 7350 PASS DP=215;AF=0.953488;SB=1;DP4=4,2,114,95 -MN908947.3 16176 . T C 49314 PASS DP=1725;AF=0.986087;SB=5;DP4=1,2,1098,624 -MN908947.3 21764 . ATACATG A 18959 PASS DP=555;AF=0.953153;SB=5;DP4=12,14,305,224;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 3969 PASS DP=122;AF=0.860656;SB=0;DP4=8,13,40,65;INDEL;HRUN=3 -MN908947.3 23063 . A T 49314 PASS DP=2333;AF=0.990999;SB=0;DP4=0,0,948,1385 -MN908947.3 23403 . A G 411 PASS DP=13;AF=0.846154;SB=0;DP4=0,0,4,8 -MN908947.3 23604 . C A 49314 PASS DP=2580;AF=0.985271;SB=0;DP4=0,0,1476,1104 -MN908947.3 23709 . C T 49314 PASS DP=1939;AF=0.91542;SB=8;DP4=2,0,720,1213 -MN908947.3 24914 . G C 49314 PASS DP=7178;AF=0.98788;SB=0;DP4=1,1,2757,4419 -MN908947.3 26467 . G C 424 PASS DP=32;AF=0.90625;SB=0;DP4=1,2,14,15 -MN908947.3 27972 . C T 10871 PASS DP=293;AF=0.989761;SB=0;DP4=0,0,141,152 -MN908947.3 28048 . G T 10671 PASS DP=288;AF=0.975694;SB=0;DP4=0,0,127,161 -MN908947.3 28111 . A G 8447 PASS DP=243;AF=0.967078;SB=0;DP4=0,0,118,124 -MN908947.3 28253 . CA C 1176 PASS DP=223;AF=0.269058;SB=155;DP4=93,70,1,59;INDEL;HRUN=1 -MN908947.3 28254 . A C 1845 PASS DP=343;AF=0.346939;SB=0;DP4=93,71,65,54 -MN908947.3 28270 . TA T 46705 PASS DP=2223;AF=0.975259;SB=10;DP4=27,29,1292,876;INDEL;HRUN=4 -MN908947.3 28280 . G C 49314 PASS DP=2252;AF=0.989343;SB=3;DP4=3,4,1326,916 -MN908947.3 28281 . A T 49314 PASS DP=2252;AF=0.988455;SB=5;DP4=3,5,1326,915 -MN908947.3 28282 . T A 49314 PASS DP=2362;AF=0.992803;SB=1;DP4=3,3,1372,980 -MN908947.3 28677 . C T 49314 PASS DP=6147;AF=0.986009;SB=0;DP4=2,4,2149,3990 -MN908947.3 29577 . T A 159 PASS DP=57;AF=0.175439;SB=0;DP4=24,23,5,5 diff --git a/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter02.vcf b/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter02.vcf deleted file mode 100644 index 8297dea..0000000 --- a/benchmark/ERR5514762/ERR5514762.preprocessed.lofreq.vcf.filter02.vcf +++ /dev/null @@ -1,47 +0,0 @@ -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20210607 -##source=lofreq call --min-bq 20 --min-alt-bq 20 --min-mq 20 --ref ../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa --call-indels --out ERR5514762/ERR5514762.preprocessed.lofreq.vcf ERR5514762/ERR5514762.preprocessed.lofreq.bam -##reference=../test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= 0.001000"> -##FILTER= -##FILTER= -##contig= -##bcftools_filterVersion=1.10.2+htslib-1.10.2 -##bcftools_filterCommand=filter --exclude 'INFO/AF < 0.2' ./ERR5514762/ERR5514762.preprocessed.lofreq.vcf.gz; Date=Tue Jun 8 07:28:18 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO -MN908947.3 241 . C T 4980 PASS DP=143;AF=0.965035;SB=0;DP4=0,0,72,71 -MN908947.3 913 . C T 2623 PASS DP=74;AF=0.945946;SB=0;DP4=1,2,31,40 -MN908947.3 2453 . C T 6346 PASS DP=177;AF=0.966102;SB=0;DP4=1,1,74,101 -MN908947.3 3037 . C T 8470 PASS DP=229;AF=0.9869;SB=0;DP4=0,0,102,127 -MN908947.3 5388 . C A 49314 PASS DP=3827;AF=0.977267;SB=2;DP4=2,0,2409,1410 -MN908947.3 5986 . C T 2665 PASS DP=74;AF=0.986486;SB=0;DP4=0,0,49,25 -MN908947.3 14408 . C T 42303 PASS DP=1143;AF=0.988626;SB=0;DP4=0,0,562,580 -MN908947.3 15279 . C T 7350 PASS DP=215;AF=0.953488;SB=1;DP4=4,2,114,95 -MN908947.3 16176 . T C 49314 PASS DP=1725;AF=0.986087;SB=5;DP4=1,2,1098,624 -MN908947.3 21764 . ATACATG A 18959 PASS DP=555;AF=0.953153;SB=5;DP4=12,14,305,224;INDEL;HRUN=1 -MN908947.3 21990 . TTTA T 3969 PASS DP=122;AF=0.860656;SB=0;DP4=8,13,40,65;INDEL;HRUN=3 -MN908947.3 23063 . A T 49314 PASS DP=2333;AF=0.990999;SB=0;DP4=0,0,948,1385 -MN908947.3 23403 . A G 411 PASS DP=13;AF=0.846154;SB=0;DP4=0,0,4,8 -MN908947.3 23604 . C A 49314 PASS DP=2580;AF=0.985271;SB=0;DP4=0,0,1476,1104 -MN908947.3 23709 . C T 49314 PASS DP=1939;AF=0.91542;SB=8;DP4=2,0,720,1213 -MN908947.3 24914 . G C 49314 PASS DP=7178;AF=0.98788;SB=0;DP4=1,1,2757,4419 -MN908947.3 26467 . G C 424 PASS DP=32;AF=0.90625;SB=0;DP4=1,2,14,15 -MN908947.3 27972 . C T 10871 PASS DP=293;AF=0.989761;SB=0;DP4=0,0,141,152 -MN908947.3 28048 . G T 10671 PASS DP=288;AF=0.975694;SB=0;DP4=0,0,127,161 -MN908947.3 28111 . A G 8447 PASS DP=243;AF=0.967078;SB=0;DP4=0,0,118,124 -MN908947.3 28253 . CA C 1176 PASS DP=223;AF=0.269058;SB=155;DP4=93,70,1,59;INDEL;HRUN=1 -MN908947.3 28254 . A C 1845 PASS DP=343;AF=0.346939;SB=0;DP4=93,71,65,54 -MN908947.3 28270 . TA T 46705 PASS DP=2223;AF=0.975259;SB=10;DP4=27,29,1292,876;INDEL;HRUN=4 -MN908947.3 28280 . G C 49314 PASS DP=2252;AF=0.989343;SB=3;DP4=3,4,1326,916 -MN908947.3 28281 . A T 49314 PASS DP=2252;AF=0.988455;SB=5;DP4=3,5,1326,915 -MN908947.3 28282 . T A 49314 PASS DP=2362;AF=0.992803;SB=1;DP4=3,3,1372,980 -MN908947.3 28677 . C T 49314 PASS DP=6147;AF=0.986009;SB=0;DP4=2,4,2149,3990 diff --git a/benchmark/ERR5514762/ERR5514762.vcf b/benchmark/ERR5514762/ERR5514762.vcf deleted file mode 100644 index 20fce58..0000000 --- a/benchmark/ERR5514762/ERR5514762.vcf +++ /dev/null @@ -1,59 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##bcftoolsVersion=1.12+htslib-1.12 -##bcftoolsCommand=mpileup -E -d 0 -A -f /home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -a AD /home/priesgo/src/covigator-ngs-pipeline/benchmark/ERR5514762/ERR5514762.preprocessed.bam -##reference=file:///home/priesgo/.nextflow/assets/tron-bioinformatics/covigator-ngs-pipeline/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.12+htslib-1.12 -##bcftools_callCommand=call -mv --ploidy 1 -Ov -o ERR5514762.vcf; Date=Mon Jun 7 16:02:45 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal -MN908947.3 241 . C T 225.417 . DP=49;VDB=0.908417;SGB=-0.693143;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,28,10;MQ=60 GT:PL:AD 1:255,0:0,38 -MN908947.3 913 . C T 228.31 . DP=31;VDB=0.0238607;SGB=-0.693054;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,22,6;MQ=60 GT:PL:AD 1:255,0:1,28 -MN908947.3 2453 . C T 228.392 . DP=58;VDB=0.368441;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,31,19;MQ=60 GT:PL:AD 1:255,0:1,50 -MN908947.3 3037 . C T 225.417 . DP=58;VDB=0.285883;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,32,16;MQ=60 GT:PL:AD 1:255,0:0,48 -MN908947.3 5087 . A G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60 GT:PL:AD 1:37,0:0,1 -MN908947.3 5388 . C A 225.417 . DP=103;VDB=0.125998;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,97,3;MQ=60 GT:PL:AD 1:255,0:0,100 -MN908947.3 5986 . C T 225.417 . DP=34;VDB=0.389335;SGB=-0.693054;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,24,4;MQ=60 GT:PL:AD 1:255,0:0,28 -MN908947.3 7414 . G T 4.38466 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=32 GT:PL:AD 1:32,0:0,1 -MN908947.3 14408 . C T 225.417 . DP=80;VDB=0.0239241;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,44,26;MQ=60 GT:PL:AD 1:255,0:0,70 -MN908947.3 15279 . C T 228.38 . DP=53;VDB=0.565758;SGB=-0.693145;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=1,0,34,6;MQ=60 GT:PL:AD 1:255,0:1,40 -MN908947.3 16176 . T C 225.417 . DP=48;VDB=0.00966111;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,7;MQ=60 GT:PL:AD 1:255,0:0,45 -MN908947.3 21764 . ATACATGT AT 228.332 . INDEL;IDV=58;IMF=0.95082;DP=61;VDB=0.0190795;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=3,1,43,14;MQ=60 GT:PL:AD 1:255,0:4,57 -MN908947.3 21990 . TTTATTA TTTA 192.24 . INDEL;IDV=26;IMF=0.787879;DP=33;VDB=2.8013e-06;SGB=-0.692914;MQSB=0.978183;MQ0F=0;AC=1;AN=1;DP4=4,4,18,7;MQ=58 GT:PL:AD 1:255,36:8,25 -MN908947.3 23063 . A T 225.417 . DP=104;VDB=0.759419;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,79,23;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 23271 . C A 115.139 . DP=8;VDB=0.250121;SGB=-0.616816;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,5,1;MQ=60 GT:PL:AD 1:154,12:1,6 -MN908947.3 23403 . A G 198.421 . DP=10;VDB=0.326789;SGB=-0.636426;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,5,2;MQ=60 GT:PL:AD 1:228,0:0,6 -MN908947.3 23604 . C A 225.417 . DP=94;VDB=0.13874;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,73,19;MQ=60 GT:PL:AD 1:255,0:0,92 -MN908947.3 23709 . C T 225.417 . DP=83;VDB=0.0336649;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,55,23;MQ=60 GT:PL:AD 1:255,0:0,78 -MN908947.3 24506 . T G 8.13869 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,1,0;MQ=60 GT:PL:AD 1:37,0:0,1 -MN908947.3 24914 . G C 225.422 . DP=107;VDB=0.189845;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,95,8;MQ=60 GT:PL:AD 1:255,0:0,102 -MN908947.3 27972 . C T 225.417 . DP=72;VDB=0.514775;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,41,20;MQ=60 GT:PL:AD 1:255,0:0,61 -MN908947.3 28048 . G T 225.417 . DP=65;VDB=0.262381;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,38,19;MQ=60 GT:PL:AD 1:255,0:0,57 -MN908947.3 28111 . A G 225.417 . DP=48;VDB=0.288894;SGB=-0.693145;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,31,10;MQ=60 GT:PL:AD 1:255,0:0,41 -MN908947.3 28280 . G C 228.319 . DP=42;VDB=0.00821796;SGB=-0.693141;RPB=0.27027;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28281 . A T 228.292 . DP=42;VDB=0.00728612;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=0.972973;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28282 . T A 228.296 . DP=43;VDB=0.00647971;SGB=-0.693141;RPB=0.256757;MQB=0.972973;MQSB=0.985376;BQB=1;MQ0F=0;AC=1;AN=1;DP4=2,0,26,11;MQ=59 GT:PL:AD 1:255,0:2,37 -MN908947.3 28677 . C T 228.405 . DP=99;VDB=0.432583;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=1;AN=1;DP4=0,1,87,7;MQ=60 GT:PL:AD 1:255,0:1,94 -MN908947.3 28881 . G A 9.88514 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:39,0:0,1 -MN908947.3 28882 . G A 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 -MN908947.3 28883 . G C 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 -MN908947.3 28977 . C T 8.99921 . DP=1;SGB=-0.379885;MQ0F=0;AC=1;AN=1;DP4=0,0,0,1;MQ=60 GT:PL:AD 1:38,0:0,1 diff --git a/main.nf b/main.nf index 46ddecb..9333068 100755 --- a/main.nf +++ b/main.nf @@ -99,7 +99,7 @@ if (library == "paired") { """ # --input_files needs to be forced, otherwise it is inherited from profile in tests - nextflow run tron-bioinformatics/tronflow-bwa -r ${params.tronflow_bwa_version} \ + nextflow run ${params.tronflow_bwa} \ --input_name ${name} \ --input_fastq1 ${fastq1} \ --input_fastq2 ${fastq2} \ @@ -154,8 +154,7 @@ else { """ # --input_files needs to be forced, otherwise it is inherited from profile in tests - nextflow run tron-bioinformatics/tronflow-bwa \ - -r ${params.tronflow_bwa_version} \ + nextflow run ${params.tronflow_bwa} \ --input_name ${name} \ --input_fastq1 ${fastq1} \ --input_files false \ @@ -188,8 +187,7 @@ process bamPreprocessing { """ # --input_files, --known_indels1 and --known_indels2 needs to be forced, otherwise it is inherited from test profile - nextflow run tron-bioinformatics/tronflow-bam-preprocessing \ - -r ${params.tronflow_bam_preprocessing_version} \ + nextflow run ${params.tronflow_bam_preprocessing} \ --input_bam ${bam} \ --input_files false \ --output . \ @@ -352,8 +350,7 @@ process variantNormalization { """ # --input_files needs to be forced, otherwise it is inherited from profile in tests - nextflow run tron-bioinformatics/tronflow-variant-normalization \ - -r ${params.tronflow_variant_normalization_version} \ + nextflow run ${params.tronflow_variant_normalization} \ --input_vcf ${vcf} \ --input_files false \ --output . \ diff --git a/nextflow.config b/nextflow.config index 0c9ce45..f4dd4f5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,9 +4,9 @@ * ------------------------------------------------- */ -params.tronflow_bwa_version = "v1.4.0" -params.tronflow_bam_preprocessing_version = "v1.5.0" -params.tronflow_variant_normalization_version = "v1.1.0" +params.tronflow_bwa = "tron-bioinformatics/tronflow-bwa -r v1.4.0" +params.tronflow_bam_preprocessing = "tron-bioinformatics/tronflow-bam-preprocessing -r v1.5.0" +params.tronflow_variant_normalization = "tron-bioinformatics/tronflow-variant-normalization -r v1.1.0" params.reference = "$baseDir/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa" params.gff = "$baseDir/reference/Sars_cov_2.ASM985889v3.101.gff3" @@ -36,7 +36,7 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -VERSION = '0.3.0' +VERSION = '0.3.1' manifest { name = 'TRON-Bioinformatics/covigator-ngs-pipeline'