diff --git a/tests/test_data/ref_transcript_mismatch_reporter/input.protein_coding.vcf b/tests/test_data/ref_transcript_mismatch_reporter/input.protein_coding.vcf
new file mode 100644
index 0000000..fadde49
--- /dev/null
+++ b/tests/test_data/ref_transcript_mismatch_reporter/input.protein_coding.vcf
@@ -0,0 +1,149 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
+##FILTER=<ID=base_qual,Description="alt median base quality">
+##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
+##FILTER=<ID=contamination,Description="contamination">
+##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
+##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
+##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
+##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
+##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
+##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
+##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
+##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
+##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
+##FILTER=<ID=orientation,Description="Orientation bias detected by the orientation bias mixture model">
+##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
+##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
+##FILTER=<ID=slippage,Description="Variant near filtered variant on same haplotype.">
+##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
+##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
+##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##INFO=<ID=AS_FilterStatus,Number=1,Type=String,Description="Filter status for each allele, as assessed by ApplyRecalibration. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
+##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
+##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
+##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
+##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
+##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
+##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
+##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
+##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
+##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
+##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
+##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
+##SentieonCommandLine.TNfilter=<ID=TNfilter,Version="sentieon-genomics-202112.05",Date="2024-01-31T08:17:32Z",CommandLine="/sga_dev/zb-liaowanjun/sentieon-genomics-202112.05/libexec/driver -r /data2/data_share/pzx/reference/hs37d5/hs37d5.fa --algo TNfilter --tumor_sample T-4032 --normal_sample PB-4032 -v /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointTMP.vcf /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointunfiltered.vcf">
+##SentieonCommandLine.TNhaplotyper2=<ID=TNhaplotyper2,Version="sentieon-genomics-202112.05",Date="2024-01-31T06:48:28Z",CommandLine="/sga_dev/zb-liaowanjun/sentieon-genomics-202112.05/libexec/driver -t 15 -r /data2/data_share/pzx/reference/hs37d5/hs37d5.fa -i /data2/dev_projects/xmy/TNB/validation_data/test1/PRJNA298330/T-4032/realigned/T-4032_final.bam -i /data2/dev_projects/xmy/TNB/validation_data/test1/PRJNA298330/PB-4032/realigned/PB-4032_final.bam --interval /sga_dev/panel_validation/V710_panel/bed/sort_KST700_v3_pd100_merged.bed --algo TNhaplotyper2 --call_germline_sites --min_init_tumor_lod 0 --min_tumor_lod 0.5 --prune_factor -1 --min_normal_lod 0 --tumor_sample T-4032 --normal_sample PB-4032 /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointTMP.vcf">
+##contig=<ID=chr1,length=249250621,assembly=b37>
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+##contig=<ID=NC_007605,length=171823,assembly=b37>
+##contig=<ID=hs37d5,length=35477943,assembly=b37>
+##reference=/xx/hs37d5.fa
+##tumor_sample=Tumor-666
+##normal_sample=Normal-666
+##bcftools_filterVersion=1.11+htslib-1.11
+##VEP="v103" time="2024-02-01 13:52:04" cache=/xx/homo_sapiens_refseq/103_GRCh37" ensembl-variation=103.06320c4 ensembl=103.4c8d44a ensembl-io=103.353f93a ensembl-funcgen=103.b53bef4 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" refseq="2019-10-24 23:10:14 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|TSL|REFSEQ_MATCH|REFSEQ_OFFSET|GIVEN_REF|USED_REF|BAM_EDIT|HGVS_OFFSET|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|FrameshiftSequence|WildtypeProtein">
+##FrameshiftSequence=Predicted sequence for frameshift mutations
+##WildtypeProtein=The normal, non-mutated protein sequence
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Normal-666	Tumor-666
+chr12	48238361	.	G	GCCTCAATGAGGAGCACTCCAAGCAGTACCGCTGCCTCTCCTTCCAGCC	.	clustered_events	AS_FilterStatus=SITE;AS_SB_TABLE=101,4|1,6;DP=118;ECNT=5;GERMQ=93;MBQ=37,34;MFRL=52,194;MMQ=60,60;MPOS=49;NALOD=1.48;NLOD=8.75;POPAF=6;TLOD=19.3;CSQ=CCTCAATGAGGAGCACTCCAAGCAGTACCGCTGCCTCTCCTTCCAGCC|stop_gained&protein_altering_variant|HIGH|VDR|7421|Transcript|NM_001364085.1|protein_coding|10/10||NM_001364085.1:c.1451_1452insGGCTGGAAGGAGAGGCAGCGGTACTGCTTGGAGTGCTCCTCATTGAGG|NP_001351014.1:p.Asn484delinsLysAlaGlyArgArgGlySerGlyThrAlaTrpSerAlaProHisTer|1611-1612|1451-1452|484|N/KAGRRGSGTAWSAPH*G|aac/aaGGCTGGAAGGAGAGGCAGCGGTACTGCTTGGAGTGCTCCTCATTGAGGc|||-1||EntrezGene|||rseq_mrna_nonmatch&rseq_5p_mismatch||||OK|||||||||||||||MEAMAASTSLPDPGDFDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHCITSSDMMDSSSFSNLDLSEEDSDDPSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEISLGQPVAVPGWGCSSRATCQARGWRLLSSPPHPVWGSAPPLPPPLSTQPILSPVQPNPFPAGFSPVP	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:29,0:0.0318:29:17,0:12,0:29,0,0,0	0/1:76,7:0.0936:83:57,1:19,0:72,4,1,6
diff --git a/tests/test_data/ref_transcript_mismatch_reporter/output.protein_coding.filtered.vcf b/tests/test_data/ref_transcript_mismatch_reporter/output.protein_coding.filtered.vcf
new file mode 100644
index 0000000..d3cb843
--- /dev/null
+++ b/tests/test_data/ref_transcript_mismatch_reporter/output.protein_coding.filtered.vcf
@@ -0,0 +1,148 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
+##FILTER=<ID=base_qual,Description="alt median base quality">
+##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
+##FILTER=<ID=contamination,Description="contamination">
+##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
+##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
+##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
+##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
+##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
+##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
+##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
+##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
+##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
+##FILTER=<ID=orientation,Description="Orientation bias detected by the orientation bias mixture model">
+##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
+##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
+##FILTER=<ID=slippage,Description="Variant near filtered variant on same haplotype.">
+##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
+##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
+##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##INFO=<ID=AS_FilterStatus,Number=1,Type=String,Description="Filter status for each allele, as assessed by ApplyRecalibration. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
+##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
+##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
+##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
+##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
+##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
+##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
+##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
+##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
+##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
+##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
+##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
+##SentieonCommandLine.TNfilter=<ID=TNfilter,Version="sentieon-genomics-202112.05",Date="2024-01-31T08:17:32Z",CommandLine="/sga_dev/zb-liaowanjun/sentieon-genomics-202112.05/libexec/driver -r /data2/data_share/pzx/reference/hs37d5/hs37d5.fa --algo TNfilter --tumor_sample T-4032 --normal_sample PB-4032 -v /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointTMP.vcf /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointunfiltered.vcf">
+##SentieonCommandLine.TNhaplotyper2=<ID=TNhaplotyper2,Version="sentieon-genomics-202112.05",Date="2024-01-31T06:48:28Z",CommandLine="/sga_dev/zb-liaowanjun/sentieon-genomics-202112.05/libexec/driver -t 15 -r /data2/data_share/pzx/reference/hs37d5/hs37d5.fa -i /data2/dev_projects/xmy/TNB/validation_data/test1/PRJNA298330/T-4032/realigned/T-4032_final.bam -i /data2/dev_projects/xmy/TNB/validation_data/test1/PRJNA298330/PB-4032/realigned/PB-4032_final.bam --interval /sga_dev/panel_validation/V710_panel/bed/sort_KST700_v3_pd100_merged.bed --algo TNhaplotyper2 --call_germline_sites --min_init_tumor_lod 0 --min_tumor_lod 0.5 --prune_factor -1 --min_normal_lod 0 --tumor_sample T-4032 --normal_sample PB-4032 /sga_dev/zb-liaowanjun/sample36_joint/T-4032_PB-4032/matched_tmp/T-4032_jointTMP.vcf">
+##contig=<ID=chr1,length=249250621,assembly=b37>
+##contig=<ID=chr2,length=243199373,assembly=b37>
+##contig=<ID=chr3,length=198022430,assembly=b37>
+##contig=<ID=chr4,length=191154276,assembly=b37>
+##contig=<ID=chr5,length=180915260,assembly=b37>
+##contig=<ID=chr6,length=171115067,assembly=b37>
+##contig=<ID=chr7,length=159138663,assembly=b37>
+##contig=<ID=chr8,length=146364022,assembly=b37>
+##contig=<ID=chr9,length=141213431,assembly=b37>
+##contig=<ID=chr10,length=135534747,assembly=b37>
+##contig=<ID=chr11,length=135006516,assembly=b37>
+##contig=<ID=chr12,length=133851895,assembly=b37>
+##contig=<ID=chr13,length=115169878,assembly=b37>
+##contig=<ID=chr14,length=107349540,assembly=b37>
+##contig=<ID=chr15,length=102531392,assembly=b37>
+##contig=<ID=chr16,length=90354753,assembly=b37>
+##contig=<ID=chr17,length=81195210,assembly=b37>
+##contig=<ID=chr18,length=78077248,assembly=b37>
+##contig=<ID=chr19,length=59128983,assembly=b37>
+##contig=<ID=chr20,length=63025520,assembly=b37>
+##contig=<ID=chr21,length=48129895,assembly=b37>
+##contig=<ID=chr22,length=51304566,assembly=b37>
+##contig=<ID=chrX,length=155270560,assembly=b37>
+##contig=<ID=chrY,length=59373566,assembly=b37>
+##contig=<ID=chrM,length=16569,assembly=b37>
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+##contig=<ID=GL000193.1,length=189789,assembly=b37>
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+##contig=<ID=GL000225.1,length=211173,assembly=b37>
+##contig=<ID=GL000192.1,length=547496,assembly=b37>
+##contig=<ID=NC_007605,length=171823,assembly=b37>
+##contig=<ID=hs37d5,length=35477943,assembly=b37>
+##reference=/xx/hs37d5.fa
+##tumor_sample=Tumor-666
+##normal_sample=Normal-666
+##bcftools_filterVersion=1.11+htslib-1.11
+##VEP="v103" time="2024-02-01 13:52:04" cache=/xx/homo_sapiens_refseq/103_GRCh37" ensembl-variation=103.06320c4 ensembl=103.4c8d44a ensembl-io=103.353f93a ensembl-funcgen=103.b53bef4 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" refseq="2019-10-24 23:10:14 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|TSL|REFSEQ_MATCH|REFSEQ_OFFSET|GIVEN_REF|USED_REF|BAM_EDIT|HGVS_OFFSET|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|FrameshiftSequence|WildtypeProtein">
+##FrameshiftSequence=Predicted sequence for frameshift mutations
+##WildtypeProtein=The normal, non-mutated protein sequence
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Normal-666	Tumor-666
diff --git a/tests/test_ref_transcript_mismatch_reporter.py b/tests/test_ref_transcript_mismatch_reporter.py
index 7bf689f..d5c0917 100644
--- a/tests/test_ref_transcript_mismatch_reporter.py
+++ b/tests/test_ref_transcript_mismatch_reporter.py
@@ -80,3 +80,15 @@ def test_no_protein_position_filter(self):
         ref_transcript_mismatch_reporter.main(command)
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.no_protein_pos.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
+
+    def test_protein_coding(self):
+        temp_path = tempfile.TemporaryDirectory()
+        os.symlink(os.path.join(self.test_data_dir, 'input.protein_coding.vcf'), os.path.join(temp_path.name, 'input.vcf'))
+        command = [
+            os.path.join(temp_path.name, 'input.vcf'),
+            "-f",
+            "hard"
+        ]
+        ref_transcript_mismatch_reporter.main(command)
+        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.protein_coding.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
+        temp_path.cleanup()
diff --git a/vatools/ref_transcript_mismatch_reporter.py b/vatools/ref_transcript_mismatch_reporter.py
index 3e2d9ac..e505889 100644
--- a/vatools/ref_transcript_mismatch_reporter.py
+++ b/vatools/ref_transcript_mismatch_reporter.py
@@ -6,7 +6,7 @@
 from collections import OrderedDict
 import logging
 
-def resolve_consequence(consequence_string):
+def resolve_consequence(consequence_string, allele):
     if '&' in consequence_string:
         consequences = {consequence.lower() for consequence in consequence_string.split('&')}
     elif '.' in consequence_string:
@@ -26,14 +26,17 @@ def resolve_consequence(consequence_string):
         consequence = 'inframe_ins'
     elif 'inframe_deletion' in consequences:
         consequence = 'inframe_del'
-    #TODO add support for protein_altering_variant
-    #elif 'protein_altering_variant' in consequences:
-    #    if len(ref) > len(alt) and (len(ref) - len(alt)) % 3 == 0:
-    #        consequence = 'inframe_del'
-    #    elif len(alt) > len(ref) and (len(alt) - len(ref)) % 3 == 0:
-    #        consequence = 'inframe_ins'
-    #    else:
-    #        consequence = None
+    elif 'protein_altering_variant' in consequences:
+        if '-' in allele:
+            allele = allele.replace('-', '')
+            if len(allele) % 3 == 0:
+                consequence = 'inframe_del'
+            else:
+                consequence = None
+        elif len(allele) % 3 == 0:
+            consequence = 'inframe_ins'
+        else:
+            consequence = None
     else:
         consequence = None
     return consequence
@@ -129,6 +132,8 @@ def main(args_input = sys.argv[1:]):
             for transcript in entry.INFO['CSQ']:
                 transcript_count += 1
                 for key, value in zip(csq_format, transcript.split('|')):
+                    if key == 'Allele':
+                        allele = value
                     if key == 'WildtypeProtein':
                         full_wildtype_sequence = value
                     if key == 'Amino_acids':
@@ -144,7 +149,7 @@ def main(args_input = sys.argv[1:]):
                             if protein_position == '-':
                                 protein_position = value.split('/')[1]
                     if key == 'Consequence':
-                        variant_type = resolve_consequence(value)
+                        variant_type = resolve_consequence(value, allele)
                     if key == 'Feature':
                         transcript_id = value