Repository: griffithlab/VAtools (language: python)

Issue:
ValueError: invalid literal for int() with base 10
Hello, recently I've found the mismatch issue with my RNAseq data.
Basically I have both normal & tumor RNAseq data. I did the variant calling following the pipeline below:
1. STAR (index using GENCODE GRCh38.primary_assembly.genome.fa & gencode.v40.annotation.gtf)
2. GATK (GRCh38.primary_assembly.genome.fa provided as fasta)
  2a. MarkDuplicatesSpark
  2b. SplitNCigarReads
  2c. BQSR
  2d. Mutect2
3. VEP (version 106)
```
    vep --input_file vcf_files/${sample}_RNA_match_RNA_somatic.filtered.vcf.gz \
        --format vcf \
        --output_file vep/${sample}_RNA_match_RNA_somatic.filtered.vep.vcf \
        --vcf --symbol --terms SO --tsl --hgvs \
        --fasta reference/vep/homo_sapiens/106_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
        --offline --cache --dir_cache reference/vep/ \
        --plugin Frameshift --plugin Wildtype --dir_plugins reference/vep/plugins/ \
        --synonyms reference/vep/homo_sapiens/106_GRCh38/chr_synonyms.txt
```
4. pVACtools (version 3.0.1)
```
	pvacseq run --iedb-install-directory ~/.conda/miniconda/4.9/envs/neo/ \
              --binding-threshold 500 --n-threads 24 \
              --net-chop-method "cterm" --netmhc-stab --exclude-NAs \
              --normal-sample-name ${sample}_N \
              vep/${sample}_RNA_match_RNA_somatic.filtered.vep.vcf \
              ${sample} ${hla1},${hla2} \
              MHCflurry MHCnuggetsI NetMHC NetMHCpan \
              pvacseq/${sample}_RNA_match_RNA 
```
The first issue is when running VEP, I got the follow message for a few lines, but it still generated a VEP annotated vcf.
```
Use of uninitialized value in numeric lt (<) at /hpctmp/renyi04/reference/vep/plugins/Frameshift.pm line 129, <$fh> line 5840.
Use of uninitialized value in numeric lt (<) at /hpctmp/renyi04/reference/vep/plugins/Frameshift.pm line 129, <$fh> line 5840.
Use of uninitialized value in addition (+) at /hpctmp/renyi04/reference/vep/plugins/Frameshift.pm line 129, <$fh> line 5840.
```
The second error is when I run pvacseq, I got warnings and errors below:

```
KI270733.1 135027 C CT
Variant doesn't have protein position information. Skipping.
KI270733.1 135027 C CCG
Variant doesn't have protein position information. Skipping.
KI270733.1 135028 CGCGCGCGCGGGAGGGCGCGTGCCCCG C
Variant doesn't have protein position information. Skipping.
KI270733.1 168056 T G ENST00000615130
Variant doesn't have protein position information. Skipping.
KI270733.1 177433 G GGGC ENST00000618998
Completed
Generating Variant Peptide FASTA and Key File
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2208.EIF4E2.ENST00000258416.inframe_del.176-177QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2209.EIF4E2.ENST00000409098.inframe_del.176-177QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2210.EIF4E2.ENST00000409167.inframe_del.131-132QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2211.EIF4E2.ENST00000409322.inframe_del.131-132QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2212.EIF4E2.ENST00000409394.inframe_del.131-132QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2213.EIF4E2.ENST00000409495.inframe_del.176-177QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2214.EIF4E2.ENST00000409514.inframe_del.176-177QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2215.EIF4E2.ENST00000454501.inframe_del.171-172QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2216.EIF4E2.ENST00000687222.inframe_del.131-132QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
Warning: Amino acid change is not sane - contains multiple stops. Skipping entry 2217.EIF4E2.ENST00000690794.inframe_del.76-77QVSHP*ARLVSCVAFALLAAPDLL**FLLFLW*E/QE
ERROR: There was a mismatch between the actual wildtype amino acid sequence (VHILGEPRPHLFGQMFVRLQLLRAVREVLHTGLAMLGL) and the expected amino acid sequence (VHILGVSTQQNGVGRAERYRVKAKEAEDETSRPFLFQE). Did you use the same reference build version for VEP that you used for creating the VCF?
{'chromosome_name': 'chr3', 'start': '49015706', 'stop': '49015817', 'reference': 'TCCTGAAAGAGAAAGGGCCTGCTGGTCTCATCCTCTGCTTCCTTTGCCTTTACCCTATACCTCTCTGCACGTCCCACCCCATTTTGCTGTGTGCTCACCCCCAGGATGTGTA', 'variant': 'T', 'gene_name': 'DALRD3', 'transcript_name': 'ENST00000313778', 'transcript_support_level': '2', 'amino_acid_change': 'VHILGVSTQQNGVGRAERYRVKAKEAEDETSRPFLFQE/E', 'codon_change': 'gTACACATCCTGGGGGTGAGCACACAGCAAAATGGGGTGGGACGTGCAGAGAGGTATAGGGTAAAGGCAAAGGAAGCAGAGGATGAGACCAGCAGGCCCTTTCTCTTTCAGGag/gag', 'ensembl_gene_id': 'ENSG00000178149', 'hgvsc': 'ENST00000313778.9:c.998_1012del', 'hgvsp': 'ENSP00000323265.5:p.Val333_Gln337del', 'wildtype_amino_acid_sequence': 'MLTFLQQLRVDWPAASERASSHTLRSHALEELTSANDGRTLSPGILGRLCLKELVEEQGRTAGYDPNLDNCLVTEDLLSVLAELQEALWHWPEDSHPGLAGASDTGTGGCLVVHVVSCEEEFQQQKLDLLWQKLVDKAPLRQKHLICGPVKVAGAPGTLMTAPEYYEFRHTQVCKASALKHGGDLAQDPAWTEIFGVLSVATIKFEMLSTAPQSQLFLALADSSISTKGTKSGTFVMYNCARLATLFESYKCSMEQGLYPTFPPVSSLDFSLLHDEGEWLLLFNSILPFPDLLSRTAVLDCTAPGLHIAVRTEMICKFLVQLSMDFSSYYNRVHILGEPRPHLFGQMFVRLQLLRAVREVLHTGLAMLGLPPLSHI', 'frameshift_amino_acid_sequence': '', 'fusion_amino_acid_sequence': '', 'variant_type': 'inframe_del', 'protein_position': '333-338', 'transcript_expression': 'NA', 'gene_expression': 'NA', 'normal_depth': 'NA', 'normal_vaf': 'NA', 'tdna_depth': '473', 'tdna_vaf': '0.016', 'trna_depth': 'NA', 'tr
[CV023_RNA_match_RNA_somatic.filtered.vep.vcf.zip](https://github.com/griffithlab/pVACtools/files/9018016/CV023_RNA_match_RNA_somatic.filtered.vep.vcf.zip)
na_vaf': 'NA', 'index': '2823.DALRD3.ENST00000313778.inframe_del.333-338VHILGVSTQQNGVGRAERYRVKAKEAEDETSRPFLFQE/E', 'protein_length_change': ''}
```

I tried to use VAtools (5.0.1) ref-transcript-mismatch-reporter to exclude the mismatch. But got the error after it generated some entries

```
Traceback (most recent call last):
  File "/home/svu/renyi04/.conda/miniconda/4.9/envs/neo/bin/ref-transcript-mismatch-reporter", line 8, in <module>
    sys.exit(main())
  File "/home/svu/renyi04/.conda/miniconda/4.9/envs/neo/lib/python3.8/site-packages/vatools/ref_transcript_mismatch_reporter.py", line 162, in main
    position = int(protein_position.split('-', 1)[0]) - 1
ValueError: invalid literal for int() with base 10: ''
```


Last, after I removed the mismatched entries mannually (about 4-7 in different samples), pVACtools worked.

I saw the same issue about VAtools but it should be solved in the lastest version. Any suggestion how I can solve the issue?

My vep.vcf is attached
[CV023_RNA_match_RNA_somatic.filtered.vep.vcf.zip](https://github.com/griffithlab/pVACtools/files/9018027/CV023_RNA_match_RNA_somatic.filtered.vep.vcf.zip)


Discussion / hints:

Fix patch:
diff --git a/vatools/ref_transcript_mismatch_reporter.py b/vatools/ref_transcript_mismatch_reporter.py
index 311e5a5..c74e2ce 100644
--- a/vatools/ref_transcript_mismatch_reporter.py
+++ b/vatools/ref_transcript_mismatch_reporter.py
@@ -146,7 +146,10 @@ def main(args_input = sys.argv[1:]):
                     if key == 'Consequence':
                         variant_type = resolve_consequence(value)
                     if key == 'Feature':
-                        transcript = value
+                        transcript_id = value
+
+                if protein_position == '':
+                    continue
 
                 if '*' in full_wildtype_sequence:
                     continue
@@ -175,7 +178,7 @@ def main(args_input = sys.argv[1:]):
                         report_entry = {
                             'CHROM': entry.CHROM,
                             'POS': entry.POS,
-                            'Transcript': transcript,
+                            'Transcript': transcript_id,
                             'Mutation Position': protein_position,
                             'Reference Genome Wildtype Amino Acid(s)': wildtype_amino_acid,
                             'Reference Transcript Wildtype Amino Acid(s)': ref_transcript_wildtype_amino_acid,


Test patch:
diff --git a/tests/test_data/ref_transcript_mismatch_reporter/input.no_protein_pos.vcf b/tests/test_data/ref_transcript_mismatch_reporter/input.no_protein_pos.vcf
new file mode 100644
index 0000000..dbdc5db
--- /dev/null
+++ b/tests/test_data/ref_transcript_mismatch_reporter/input.no_protein_pos.vcf
@@ -0,0 +1,269 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
+##FILTER=<ID=PASS,Description="Site contains at least one allele that passes filters">
+##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=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">
+##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
+##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=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele.">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##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; will always be heterozygous and is not intended to describe called alleles">
+##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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##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.">
+##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output vcf_files/CV023_RNA_match_RNA_somatic.filtered.vcf.gz --variant vcf_files/CV023_RNA_match_RNA_somatic.vcf.gz --reference /hpctmp/renyi04/reference/gencode/GRCh38.primary_assembly.genome.fa --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --microbial-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality -1 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.6.1",Date="June 29, 2022 8:30:35 AM SGT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --normal-sample CV023_N --panel-of-normals /hpctmp/renyi04/reference/gnomad/somatic-hg38_1000g_pon.hg38.vcf.gz --germline-resource /hpctmp/renyi04/reference/gnomad/somatic-hg38_af-only-gnomad.hg38.vcf.gz --output vcf_files/CV023_RNA_match_RNA_somatic.vcf.gz --input BAM/CV023_N_final.bam --input BAM/CV023_T_final.bam --reference /hpctmp/renyi04/reference/gencode/GRCh38.primary_assembly.genome.fa --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --mutect3-training-mode false --mutect3-ref-downsample 10 --mutect3-alt-downsample 20 --mutect3-non-artifact-ratio 20 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.2.6.1",Date="June 29, 2022 2:53:18 AM SGT">
+##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyVQSR. 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=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
+##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
+##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 by allele">
+##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele">
+##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele">
+##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=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
+##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
+##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
+##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=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
+##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">
+##MutectVersion=2.2
+##contig=<ID=chr1,length=248956422>
+##contig=<ID=chr2,length=242193529>
+##contig=<ID=chr3,length=198295559>
+##contig=<ID=chr4,length=190214555>
+##contig=<ID=chr5,length=181538259>
+##contig=<ID=chr6,length=170805979>
+##contig=<ID=chr7,length=159345973>
+##contig=<ID=chr8,length=145138636>
+##contig=<ID=chr9,length=138394717>
+##contig=<ID=chr10,length=133797422>
+##contig=<ID=chr11,length=135086622>
+##contig=<ID=chr12,length=133275309>
+##contig=<ID=chr13,length=114364328>
+##contig=<ID=chr14,length=107043718>
+##contig=<ID=chr15,length=101991189>
+##contig=<ID=chr16,length=90338345>
+##contig=<ID=chr17,length=83257441>
+##contig=<ID=chr18,length=80373285>
+##contig=<ID=chr19,length=58617616>
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr22,length=50818468>
+##contig=<ID=chrX,length=156040895>
+##contig=<ID=chrY,length=57227415>
+##contig=<ID=chrM,length=16569>
+##contig=<ID=GL000008.2,length=209709>
+##contig=<ID=GL000009.2,length=201709>
+##contig=<ID=GL000194.1,length=191469>
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+##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
+##normal_sample=CV023_N
+##source=FilterMutectCalls
+##source=Mutect2
+##tumor_sample=CV023_T
+##VEP="v106" time="2022-06-30 01:15:58" cache="/hpctmp/renyi04/reference/vep/homo_sapiens/106_GRCh38" ensembl-io=106.6eafdaa ensembl-funcgen=106.027e023 ensembl-variation=106.2aa7a5d ensembl=106.f4b50c6 1000genomes="phase3" COSMIC="92" ClinVar="202109" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 40" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" 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|HGVS_OFFSET|FrameshiftSequence|WildtypeProtein">
+##FrameshiftSequence=Predicted sequence for frameshift mutations
+##WildtypeProtein=The normal, non-mutated protein sequence
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CV023_N	CV023_T
+chr19	45408613	.	G	GA,GAA	.	multiallelic;normal_artifact;slippage	AS_FilterStatus=SITE|weak_evidence,strand_bias;AS_SB_TABLE=145,61|15,2|4,0;DP=240;ECNT=1;GERMQ=93;MBQ=34,34,34;MFRL=275,273,342;MMQ=60,60,60;MPOS=44,7;NALOD=-1.648e+00,1.19;NLOD=7.08,12.31;POPAF=4.31,6.00;RPA=8,9,10;RU=A;STR;STRQ=1;TLOD=15.84,4.67;CSQ=A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8:c.*1061dup||2099-2100|||||||-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8:c.*1060_*1061dup||2099-2100|||||||-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8:c.653dup|ENSP00000310966.3:p.Asn218LysfsTer58|698-699|645-646|215-216|-/X|-/A|||1||HGNC|HGNC:24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8:c.652_653dup|ENSP00000310966.3:p.Asn218LysfsTer5|698-699|653-654|218|N/X|-/AA|||1||HGNC|HGNC:24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6:c.*1061dup||1839-1840|||||||-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6:c.*1060_*1061dup||1839-1840|||||||-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC:18838|2|||,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC:18838|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC:3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC:3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC:3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC:3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1:c.659dup|ENSP00000465099.1:p.Asn220LysfsTer58|657-658|651-652|217-218|-/X|-/A|||1||HGNC|HGNC:24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1:c.658_659dup|ENSP00000465099.1:p.Asn220LysfsTer5|657-658|659-660|220|N/X|-/AA|||1||HGNC|HGNC:24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC:3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC:3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,A|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC:24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,AA|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC:24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC:3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC:3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC:3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC:3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112|37-38|-/X|-/A|||1|cds_end_NF|HGNC|HGNC:24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112||-/X|-/AA|||1|cds_end_NF|HGNC|HGNC:24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:49,2,0:0.065,0.022:51:28,1,0:6,1,0:41,2,0:30,19,2,0	0/1/2:157,15,4:0.083,0.030:176:18,2,0:111,11,4:146,13,4:115,42,17,2
diff --git a/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf b/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf
new file mode 100644
index 0000000..1e3106c
--- /dev/null
+++ b/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf
@@ -0,0 +1,269 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
+##FILTER=<ID=PASS,Description="Site contains at least one allele that passes filters">
+##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=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">
+##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
+##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=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele.">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##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; will always be heterozygous and is not intended to describe called alleles">
+##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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##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.">
+##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output vcf_files/CV023_RNA_match_RNA_somatic.filtered.vcf.gz --variant vcf_files/CV023_RNA_match_RNA_somatic.vcf.gz --reference /hpctmp/renyi04/reference/gencode/GRCh38.primary_assembly.genome.fa --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --microbial-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality -1 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.6.1",Date="June 29, 2022 8:30:35 AM SGT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --normal-sample CV023_N --panel-of-normals /hpctmp/renyi04/reference/gnomad/somatic-hg38_1000g_pon.hg38.vcf.gz --germline-resource /hpctmp/renyi04/reference/gnomad/somatic-hg38_af-only-gnomad.hg38.vcf.gz --output vcf_files/CV023_RNA_match_RNA_somatic.vcf.gz --input BAM/CV023_N_final.bam --input BAM/CV023_T_final.bam --reference /hpctmp/renyi04/reference/gencode/GRCh38.primary_assembly.genome.fa --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --mutect3-training-mode false --mutect3-ref-downsample 10 --mutect3-alt-downsample 20 --mutect3-non-artifact-ratio 20 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.2.6.1",Date="June 29, 2022 2:53:18 AM SGT">
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+##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
+##normal_sample=CV023_N
+##source=FilterMutectCalls
+##source=Mutect2
+##tumor_sample=CV023_T
+##VEP="v106" time="2022-06-30 01:15:58" cache="/hpctmp/renyi04/reference/vep/homo_sapiens/106_GRCh38" ensembl-io=106.6eafdaa ensembl-funcgen=106.027e023 ensembl-variation=106.2aa7a5d ensembl=106.f4b50c6 1000genomes="phase3" COSMIC="92" ClinVar="202109" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 40" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" 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|HGVS_OFFSET|FrameshiftSequence|WildtypeProtein">
+##FrameshiftSequence=Predicted sequence for frameshift mutations
+##WildtypeProtein=The normal, non-mutated protein sequence
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CV023_N	CV023_T
+chr19	45408613	.	G	GA,GAA	.	multiallelic;normal_artifact;slippage	AS_FilterStatus=SITE|weak_evidence,strand_bias;AS_SB_TABLE=145%2C61|15%2C2|4%2C0;DP=240;ECNT=1;GERMQ=93;MBQ=34,34,34;MFRL=275,273,342;MMQ=60,60,60;MPOS=44,7;NALOD=-1.648,1.19;NLOD=7.08,12.31;POPAF=4.31,6.0;RPA=8,9,10;RU=A;STR;STRQ=1;TLOD=15.84,4.67;CSQ=A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8%3Ac.*1061dup||2099-2100|||||||-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8%3Ac.*1060_*1061dup||2099-2100|||||||-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8%3Ac.653dup|ENSP00000310966.3%3Ap.Asn218LysfsTer58|698-699|645-646|215-216|-/X|-/A|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8%3Ac.652_653dup|ENSP00000310966.3%3Ap.Asn218LysfsTer5|698-699|653-654|218|N/X|-/AA|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6%3Ac.*1061dup||1839-1840|||||||-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6%3Ac.*1060_*1061dup||1839-1840|||||||-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC%3A18838|2|||,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC%3A18838|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC%3A3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC%3A3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC%3A3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC%3A3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1%3Ac.659dup|ENSP00000465099.1%3Ap.Asn220LysfsTer58|657-658|651-652|217-218|-/X|-/A|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1%3Ac.658_659dup|ENSP00000465099.1%3Ap.Asn220LysfsTer5|657-658|659-660|220|N/X|-/AA|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC%3A3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC%3A3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,A|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC%3A24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,AA|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC%3A24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC%3A3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC%3A3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC%3A3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC%3A3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112|37-38|-/X|-/A|||1|cds_end_NF|HGNC|HGNC%3A24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112||-/X|-/AA|||1|cds_end_NF|HGNC|HGNC%3A24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:49,2,0:0.065,0.022:51:28,1,0:6,1,0:41,2,0:30,19,2,0	0/1/2:157,15,4:0.083,0.03:176:18,2,0:111,11,4:146,13,4:115,42,17,2
diff --git a/tests/test_ref_transcript_mismatch_reporter.py b/tests/test_ref_transcript_mismatch_reporter.py
index 037b8e2..7bf689f 100644
--- a/tests/test_ref_transcript_mismatch_reporter.py
+++ b/tests/test_ref_transcript_mismatch_reporter.py
@@ -68,3 +68,15 @@ def test_hard_filter(self):
         ref_transcript_mismatch_reporter.main(command)
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.hard.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
+
+    def test_no_protein_position_filter(self):
+        temp_path = tempfile.TemporaryDirectory()
+        os.symlink(os.path.join(self.test_data_dir, 'input.no_protein_pos.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.no_protein_pos.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
+        temp_path.cleanup()