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Add per-strand allele counts when running vcf-readcount-annotator
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@susannasiebert
susannasiebert committed Oct 16, 2023
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Showing 14 changed files with 78 additions and 42 deletions.
Binary file modified tests/test_data/complex_indel.readcount.vcf.gz
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4 changes: 2 additions & 2 deletions tests/test_data/duplicate_entries_discrepant_depths.bam_readcount.vcf
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##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##source=SelectVariants
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test_duplicates_sample
chr16 78108410 . TG T . PASS AC=1;ADP=280;AF=0.5;AN=2;HET=1;HOM=0;NC=0;WT=0;set=varscan GT:ABQ:AD:ADF:ADR:DP:FREQ:GQ:PVAL:RBQ:RD:RDF:RDR:SDP 0/1:50:97:79:18:280:48.74%25:0:9.8E-1:48:102:82:20:280
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4 changes: 2 additions & 2 deletions tests/test_data/duplicate_entries_same_depths.bam_readcount.vcf
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##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
Expand Down Expand Up @@ -55,6 +53,8 @@
##source=SelectVariants
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test_duplicates_sample
chr16 78108410 . TG T . PASS AC=1;ADP=280;AF=0.5;AN=2;HET=1;HOM=0;NC=0;WT=0;set=varscan GT:ABQ:AD:ADF:ADR:DP:FREQ:GQ:PVAL:RBQ:RD:RDF:RDR:SDP 0/1:50:97:79:18:334:48.74%25:0:9.8E-1:48:102:82:20:280
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4 changes: 3 additions & 1 deletion tests/test_data/hom_ref.readcount.vcf
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##WildtypeProtein=The normal, non-mutated protein sequence
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr22 36265781 . T G . PASS AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP 0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212 0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383
chr22 36265781 . T G . PASS AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP:ADF:ADR 0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212:108,0:99,5 0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383:.:.
4 changes: 3 additions & 1 deletion tests/test_data/indel_mode.bam_readcount.vcf
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Expand Up @@ -80,9 +80,11 @@
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395
6 41754573 . C CCTT . . CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1%3Ac.861_862insCTT|ENSP00000404911.1%3Ap.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF 0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421
6 41754573 . C CCTT . . CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1%3Ac.861_862insCTT|ENSP00000404911.1%3Ap.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF:ADF:ADR 0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421:13,26:9,26
6 43250725 . GGAA G . . CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4%3Ac.2248_2250delGAA|ENSP00000259750.4%3Ap.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF 0/1:0:43,47,54,56:34:2:0,0:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS:0
22 16228619 . T C . . CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C|||| GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC 1/1:0,5:42:2:7:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60
22 18644673 . C T . . CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
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