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Commands for snps_and_indels.cwl
Ian edited this page Apr 5, 2021
·
2 revisions
/bin/sh \
-c \
'/opt/common/CentOS_6-dev/vardict/v1.5.1/bin/VarDict' \
'-E' \
'3' \
'-G' \
'./Homo_sapiens_assembly19.fasta' \
'-N' \
'ML-fgfr2-038-pl-T04' \
'-c' \
'1' \
'-b' \
'/ML-fgfr2-038-pl-T04_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam|F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam' \
'-g' \
'4' \
'-f' \
'0.0002' \
'-S' \
'2' \
'-r' \
'1' \
'./MSK-ACCESS-v1_0panelA_canonicaltargets_500buffer.bed' \
| \
'/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/testsomatic.R' \
| \
'/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl' \
'-A' \
'-N' \
'ML-fgfr2-038-pl-T04|F20' \
'-f' \
'0.0002' \
> \
ML-fgfr2-038-pl-T04.F20.vardict.vcf
/opt/common/CentOS_6/java/jdk1.7.0_75/bin/java \
-Xmx28g \
-Xms256m \
-XX:-UseGCOverheadLimit \
-jar \
/home/johnsoni/vendor_tools/muTect-1.1.5.jar \
--analysis_type \
MuTect \
--cosmic \
./CosmicCodingMuts_v67_b37_20131024__NDS.vcf \
--dbsnp \
./dbsnp_138.b37.excluding_sites_after_129.vcf \
--downsample_to_coverage \
50000 \
--downsampling_type \
NONE \
--enable_extended_output \
--fraction_contamination \
0.0005 \
--input_file:normal \
./F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--input_file:tumor \
./ML-fgfr2-038-pl-T02_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--intervals \
./MSK-ACCESS-v1_0panelA_canonicaltargets_500buffer.bed \
--minimum_mutation_cell_fraction \
0.0005 \
--normal_sample_name \
F20 \
--out \
ML-fgfr2-038-pl-T02.F20.mutect.txt \
--read_filter \
BadCigar \
--reference_sequence \
/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
--tumor_sample_name \
ML-fgfr2-038-pl-T02 \
--vcf \
ML-fgfr2-038-pl-T02.F20.mutect.vcf
filter_vardict \
--alleledepth \
1 \
--inputVcf \
./ML-fgfr2-038-pl-T04.F20.vardict.vcf \
--minqual \
0 \
--refFasta \
./Homo_sapiens_assembly19.fasta \
--totaldepth \
20 \
--tsampleName \
ML-fgfr2-038-pl-T04 \
--tnRatio \
1 \
--variantfraction \
5e-05
filter_mutect \
--alleledepth \
1 \
--inputTxt \
./ML-fgfr2-038-pl-T02.F20.mutect.txt \
--inputVcf \
./ML-fgfr2-038-pl-T02.F20.mutect.vcf \
--refFasta \
./Homo_sapiens_assembly19.fasta \
--totaldepth \
20 \
--tsampleName \
ML-fgfr2-038-pl-T02 \
--tnRatio \
1 \
--variantfraction \
5e-05
/opt/common/CentOS_6-dev/bin/current/bcftools \
concat \
--allow-overlaps \
--output \
ML-fgfr2-038-pl-T04.F20.combined-variants.vcf \
--rm-dups \
all \
./ML-fgfr2-038-pl-T04.F20.vardict_STDfilter.norm.vcf.gz \
./ML-fgfr2-038-pl-T04.F20.mutect_STDfilter.norm.vcf.gz
annotate_concat \
--anno_header \
./mutect_annotate_concat_header.txt \
--anno_with_vcf \
./ML-fgfr2-038-pl-T04.F20.mutect_STDfilter.norm.vcf.gz \
--combined_vcf \
./ML-fgfr2-038-pl-T04.F20.combined-variants.vcf
/opt/common/CentOS_6-dev/perl/perl-5.22.0/bin/perl \
/opt/common/CentOS_6-dev/vcf2maf/v1.6.16/vcf2maf.pl \
--buffer-size \
5000 \
--custom-enst \
./dmp_ACCESS-panelA-v1-isoform-overrides \
--filter-vcf \
./ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz \
--input-vcf \
./ML-fgfr2-038-pl-T02.F20.combined-variants_anno.vcf \
--maf-center \
mskcc.org \
--max-filter-ac \
10 \
--min-hom-vaf \
0.7 \
--ncbi-build \
GRCh37 \
--normal-id \
F20 \
--output-maf \
ML-fgfr2-038-pl-T02.F20.combined-variants.vep.maf \
--ref-fasta \
./Homo_sapiens_assembly19.fasta \
--retain-info \
set,TYPE,FAILURE_REASON,MUTECT \
--species \
homo_sapiens_merged \
--tumor-id \
ML-fgfr2-038-pl-T02 \
--vcf-normal-id \
F20 \
--vcf-tumor-id \
ML-fgfr2-038-pl-T02 \
--vep-data \
/opt/common/CentOS_6-dev/vep/cache/ \
--vep-forks \
4 \
--vep-path \
/opt/common/CentOS_6-dev/vep/v86/
remove_variants_by_annotation \
--dropped_NGR_output_maf \
ML-fgfr2-038-pl-T04.F20.combined-variants.vep_droppedNGRrmv.maf \
--dropped_output_maf \
ML-fgfr2-038-pl-T04.F20.combined-variants.vep_droppedrmv.maf \
--input_interval \
./dmp_ACCESS-panelA-v1-isoform-overrides \
--input_maf \
./ML-fgfr2-038-pl-T04.F20.combined-variants.vep.maf \
--kept_output_maf \
ML-fgfr2-038-pl-T04.F20.combined-variants.vep_keptrmv.maf
tag_hotspots \
--input_hotspot \
./hotspot-list-union-v1-v2_with_TERT.txt \
--input_maf \
./ML-fgfr2-038-pl-T02.F20.combined-variants.vep_keptrmv.maf \
--output_maf \
ML-fgfr2-038-pl-T02.F20.combined-variants.vep_keptrmv_taggedHotspots.maf
/bin/sh \
-c \
'./GetBaseCountsMultiSample' \
--bam ML-fgfr2-038-pl-T02:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgee5b601a-3c1d-4072-85ba-911bec4ed5b5/ML-fgfr2-038-pl-T02_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam ML-fgfr2-038-pl-T04:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgc7cea4ce-044a-4be9-839a-1908a722ce9c/ML-fgfr2-038-pl-T04_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam ML-fgfr2-038-pl-T02-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgee9e57f6-8418-46b5-b845-e75dac11277e/ML-fgfr2-038-pl-T02_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam ML-fgfr2-038-pl-T04-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg35828e43-6830-42cd-8cd4-696f92003428/ML-fgfr2-038-pl-T04_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F20:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg6678433b-9b58-47d2-bffb-7a14d1c68e58/F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F16-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg11eda5a4-b76a-4151-82f1-31c9ec552321/Donor-F16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F2-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg23fb2252-ecff-4ca7-bd2c-6d502efc813d/Donor-F2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR1-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgb0e0d464-d3ee-4928-b580-f99fd6879da0/DONOR1-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M19-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg090a3f1f-a189-4397-96e3-fb10ba3e2459/Donor-M19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F13-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg65badda8-139a-451b-a6da-2943e9ba172a/Donor-F13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F22-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg1a8880de-12b1-4e78-945d-5e57a4a0627f/Donor-F22_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR13-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga4548eb8-6823-4d77-93f7-ed886520e863/DONOR13-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F12-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg0c4804f8-b03f-49c6-938c-54211d51b2ba/Donor-F12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M10-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgef05ce07-db14-4fba-8805-ba3cd7fe5634/Donor-M10_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F19-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg9c558677-a71f-403a-ade5-6bbf461aaaef/F19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F10-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgdccba5a5-0cbd-46a1-b7ad-00cc9be809b8/Donor-F10_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M18-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg8bc21d16-a439-417f-907b-dda763a490c5/Donor-M18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F23-1-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg0b73f6cc-5e99-4eb4-821b-c99f7113bed0/F23-1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M17-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg834a0e8b-c86c-4a69-87b3-de56d280f714/Donor-M17_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M7-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg1237e013-427c-4632-9768-c959445ef5a0/Donor-M7_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F20-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg8b4a9111-4665-4bd5-ad7f-9cd4f03e86d2/Donor-F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M6-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgeb3e7788-b6c5-4b5f-8770-b8b6ec0f21a0/Donor-M6_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M15-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgf040dac6-dadc-41c7-b48c-87b26875f9f9/Donor-M15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F17-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg3bd98e58-0375-4b3b-8e6d-285726fd525d/Donor-F17_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M8-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4d50b939-d936-4f1c-a212-ba2d2cea9eb0/Donor-M8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR26-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgdbac5655-4552-4742-854e-2aa9c95403db/DONOR26-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F7-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg09878609-f67d-4fda-b4fa-517bbee213b5/Donor-F7_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR45-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg56ed2ad8-0cc7-4c3e-ad0b-133ac3020242/DONOR45-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F27-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg2c5eae41-207b-4ea0-a17f-2dacc5437e85/Donor-F27_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M21-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgce772566-dbe5-48c0-8a32-a43a7f5a2dbc/Donor-M21_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M8-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgf6298170-b0db-43fe-9b15-4166e6f6c294/M8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F19-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga0855dd5-5b0a-4d94-beb3-c88bb835b65e/Donor-F19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M6-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgc11aef73-a061-4d73-bef3-05a7ea150e7a/M6_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F8-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg66575f30-8e15-4bcb-8468-f53637f90486/Donor-F8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F14-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg02346f4c-77c3-4c05-8f18-979b50d51441/Donor-F14_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F4-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgbbd1d080-1a18-40f1-a88f-1435ca56d068/Donor-F4_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M13-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg6d5461fd-f663-4900-ba76-d296d2c3f2b7/M13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M13-1-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5350b312-41ff-4f27-9bb9-ab95f6f4d13a/M13-1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F11-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgeff62b1b-337d-45ec-862f-efc3b6801050/Donor-F11_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR24-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4ed9484b-286c-4735-ae60-b01e6ed92f80/DONOR24-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F26-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd6236797-4aa9-4c5c-b731-e3ced03cde41/Donor-F26_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M5-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7b96bdb2-676d-4e20-8126-eabedb11719a/Donor-M5_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F23-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg874217c1-a70f-4169-8d82-3359a0131108/Donor-F23_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M12-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg6e921d96-7e6f-4028-ae1f-36454073aa42/Donor-M12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M13-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg36a4f4bf-b6cb-4464-8a4a-3dc3019ccca4/Donor-M13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F18-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg8d25ce1f-a54a-45cf-aaca-50cc14257f35/Donor-F18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M22-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5c1572a5-84eb-45ec-ad02-0743182378d3/Donor-Ó22_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M3-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg24284ae6-1c78-4aad-894d-a0f136eb9250/Donor-M3_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F20-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg234e5e76-88a7-497a-a877-6e851faa2bf2/F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F1-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg201cb911-cc2e-4b5a-9aa5-88e72eb33f11/F1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F18-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgf7439628-ea4f-4524-8abc-28c1326da017/F18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M2-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg21d2642f-079a-4fb0-8ea9-67e701ea4116/Donor-M2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F25-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5ba8ea3c-e9a4-42ae-a878-76c1749d1cee/Donor-F25_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M23-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgbb2b0406-f637-457d-b1af-1106b35deb00/Donor-M23_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M9-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg2f036ce5-1223-4dbd-99b7-05a957cb70b6/Donor-M9_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M2-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg6e7aa15c-ec4f-4e10-b1a4-fc9d02427a67/M2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F16-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga81cc285-16a5-4860-8a06-3cca1b2dbf16/F16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M14-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg8bd8241e-4174-4c8a-8996-09b74f3df7c5/Donor-M14_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam DONOR23-T-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg747dd42e-ce4f-4539-ae22-6cd5853479e4/DONOR23-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M24-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg59e22b67-8c1c-4e29-adc9-59fe41699b61/Donor-M24_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F9-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd9073050-34d6-4f45-a576-a0d9a4119f95/Donor-F9_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M11-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg22098310-8130-4c0e-a9d8-7a2ff90da4b2/Donor-M11_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M1-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5c1d70c8-cae2-4975-bbec-5e441d2aa5b4/Donor-M1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F15-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg1f94aba6-6d87-4e87-8a74-555e394eeab2/Donor-F15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M16-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7b399643-8351-48f5-8558-0696276d145a/Donor-M16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F5-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgf1ccab98-b298-4098-8697-2ad92fdc34a3/Donor-F5_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam F2-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7a927759-7be1-444c-9f99-6bfb17e30d74/F2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-M20-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd191e309-f551-4756-843f-1dde34b87c26/Donor-M20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M15-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgec079cb8-6d9f-4d28-a316-dcb306b71bb9/M15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam M12-CURATED-DUPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga3bb0991-c5bb-49d7-877b-8eaa1183c1a6/M12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
--bam Donor-F23-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7bed6853-58aa-4daa-9f9b-609e0f9ba5ca/Donor-F23_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M7-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga2729333-a0ba-438c-b446-782624862158/Donor-M7_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F13-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4a512592-a486-4e40-810a-f67916c5a895/Donor-F13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M21-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg479aef12-1d5d-4cff-a744-e089e1f1c8ff/Donor-M21_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M20-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg0f908a8c-4882-49de-b688-73bc1f85dcb6/Donor-M20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F2-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg52efc5c9-dda5-40f0-b39b-b287a309b5fc/Donor-F2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M23-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg56ea435b-6973-4136-8e42-c69ca9f95ae6/Donor-M23_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M8-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7ac33b3d-b659-4d33-b899-b28a401c8328/Donor-M8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M12-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge19fbcc0-e4de-4f67-8bd1-0eabc1a237b5/Donor-M12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M2-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge9b6a33d-96af-4f15-b7c4-b5cb68f64fa0/M2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M9-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg8e6a65a8-a45e-4f5d-b7f4-458fb80cc32d/Donor-M9_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F4-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgdecd2ecc-6bd5-4d89-9ace-93d7497818fc/Donor-F4_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M13-1-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg49d093c4-2450-489f-9cc9-3f9fd379ecef/M13-1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F18-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg902c78d3-a706-4879-bd2c-f2fa44db7410/Donor-F18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M17-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg1cb92f7a-91f3-4037-b374-20ea34b8bd46/Donor-M17_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F20-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg3bc2bd8f-44ff-4985-9c15-8d9efab0da01/F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F12-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4d86d22c-c517-4c81-bb18-af9b6f3c7120/Donor-F12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M3-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5d89ad0a-b746-4cbc-8ed1-df7065efb424/Donor-M3_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M5-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge5205b75-6a98-490c-b1e7-e7eeb91867fe/Donor-M5_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F19-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg0535b415-27c2-4534-aa74-f471153e89aa/Donor-F19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F5-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg47a90ab9-bf5b-45ea-b6dc-4589addd17ff/Donor-F5_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F23-1-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg0cbfb78e-1020-4988-bc9c-ae1ce453e928/F23-1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F20-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge1ef68c9-fe8d-4b31-a747-33c3f65163e3/Donor-F20_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F1-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg57be53be-51e0-4a27-bb33-d2cc97da70cb/F1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M19-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgeb32d22c-a32e-4d87-afb2-e858f305576d/Donor-M19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR26-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5584e141-0290-41fc-810f-81ad215e5266/DONOR26-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR13-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgef619853-454a-4982-b473-41cb326a6db0/DONOR13-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F10-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg403b69ae-77eb-4ba8-93ce-10ecfb793900/Donor-F10_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F22-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgf4e48b4d-c6d0-4277-9e49-bdfefda5d72c/Donor-F22_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M12-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg90c51b27-5408-4e02-93eb-b5ed6a3d3c23/M12_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F27-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4a53bdfb-0437-4b24-8a43-7485f2537705/Donor-F27_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M6-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4480619b-0b00-4097-9591-8090a2847c1e/M6_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M2-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stga97c8537-7ddb-47a3-bf10-314b6d751b19/Donor-M2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M22-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd3e74d24-6351-4a9c-a6f4-3e0c330e0c2a/Donor-M22_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M6-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg02414b2b-bf49-451a-a825-4e1278e636de/Donor-M6_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F7-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgbc414307-6612-4852-8269-8f39d5754daf/Donor-F7_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR45-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgde833c83-209b-4332-af75-c7d367946e5f/DONOR45-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F11-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg08db9af2-a599-4ce1-8f02-f01aec3309ce/Donor-F11_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F15-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg822c014f-cffe-44df-bb9a-faf7bbd9a26c/Donor-F15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M18-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd8af8c84-68bd-4f1f-bd1a-085aa3d3541f/Donor-M18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M15-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgaaa2c62d-1d2b-42d6-bf17-a31dd2ea0cf0/Donor-M15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F19-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg5ed8b771-beae-40d2-bd0e-3117f7a35898/F19_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F14-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg9ed4a1a8-6154-402a-a8bc-a280cd0def52/Donor-F14_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F16-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg090b4030-adb4-410c-8729-edeeaefcc47f/F16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F26-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgbf581f9a-4076-4d13-8a30-57d33a7cdcbd/Donor-F26_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M14-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg728a8653-1bf9-4c41-9cdf-0f2f1aafd3e1/Donor-M14_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F18-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgb8436dc9-1e4c-4625-a92f-2ecb4ef69561/F18_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M10-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgd07b5e1c-d84a-4cd7-927e-117bf153c0d9/Donor-M10_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M11-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgc286f764-2e43-48d7-9f17-07ccf5de97eb/Donor-M11_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M16-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg46516223-6acc-497e-a4d4-56324e865a60/Donor-M16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam F2-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg94dfb43c-b9ad-4a87-b1af-699579868d8d/F2_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M13-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg61175a58-c371-4a00-bf77-b4289e8632cf/Donor-M13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F9-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg71fa48e0-2cdc-4d52-9c59-38ef97032561/Donor-F9_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M13-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg7f2d1f4a-52cf-40bd-bc87-9b1b472cf8c8/M13_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F16-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg36ed2a00-bd22-4a81-8fa3-ef1bb898428d/Donor-F16_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F8-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge429b3a7-b0ee-4454-b83a-cd276b0fce4c/Donor-F8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR24-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg6ca00942-3bf5-4cd1-86d7-e412b6dce4aa/DONOR24-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR23-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgb7da3044-077d-4461-971c-37d2ca75b1d2/DONOR23-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam DONOR1-T-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg443acd72-ce60-4bcc-9efe-da042c83421f/DONOR1-T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F17-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg953af756-6e43-4f82-9349-edd076448a7e/Donor-F17_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M8-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stgb0b8cfe8-310f-4183-a24e-b5dd7105f5a2/M8_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M1-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg80e84609-2544-4864-bb29-0a9dd3948e9a/Donor-M1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam M15-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg42f22ba0-757d-4dbb-bb1a-5c05e74897e6/M15_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-M24-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stg4c617f0a-b9f3-41c8-8dbf-d67e5341406e/Donor-M24_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
--bam Donor-F25-CURATED-SIMPLEX:/bcftools_concat_multiallelic_test/ML-fgfr2-038_multiallelic_test-0.1.0-rc5-109-g1cb28ae/tmpmuuzhc/stge55e8cd1-59f7-41f5-bdc9-44ec76d8063a/Donor-F25_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam \
'--filter_duplicate' \
'0' \
'--fragment_count' \
'1' \
'--maf' \
'./ML-fgfr2-038-pl-T04.F20.combined-variants.vep_keptrmv_taggedHotspots.maf' \
'--maq' \
'20' \
'--omaf' \
'--output' \
'ML-fgfr2-038-pl-T04.F20.combined-variants.vep_keptrmv_taggedHotspots_fillout.maf' \
'--fasta' \
'./Homo_sapiens_assembly19.fasta' \
'--thread' \
'10'
ACCESS_Filters \
--DS_curated_detect_alt_thres \
2 \
--DS_tumor_detect_alt_thres \
2 \
--anno_maf \
./ML-fgfr2-038-pl-T02.F20.combined-variants.vep_keptrmv_taggedHotspots.maf \
--curated_detect_alt_thres \
2 \
--fillout_maf \
./ML-fgfr2-038-pl-T02.F20.combined-variants.vep_keptrmv_taggedHotspots_fillout.maf \
--min_n_curated_samples_alt_detected \
2 \
--normal_TD_min \
20 \
--normal_samplename \
'' \
--normal_vaf_germline_thres \
0.3 \
--tier_one_alt_min \
3 \
--tier_two_alt_min \
5 \
--tn_ratio_thres \
2 \
--tumor_TD_min \
20 \
--tumor_detect_alt_thres \
2 \
--tumor_samplename \
ML-fgfr2-038-pl-T02 \
--tumor_vaf_germline_thres \
0
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