diff --git a/tests/test_data/complex_indel.readcount.vcf.gz b/tests/test_data/complex_indel.readcount.vcf.gz index 55d10a0..c9d54e9 100644 Binary files a/tests/test_data/complex_indel.readcount.vcf.gz and b/tests/test_data/complex_indel.readcount.vcf.gz differ diff --git a/tests/test_data/duplicate_entries_discrepant_depths.bam_readcount.vcf b/tests/test_data/duplicate_entries_discrepant_depths.bam_readcount.vcf index c319fc0..ab8a0cf 100644 --- a/tests/test_data/duplicate_entries_discrepant_depths.bam_readcount.vcf +++ b/tests/test_data/duplicate_entries_discrepant_depths.bam_readcount.vcf @@ -15,8 +15,6 @@ ##FILTER= ##FILTER= ##FORMAT= -##FORMAT= -##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= @@ -55,6 +53,8 @@ ##source=SelectVariants ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #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 diff --git a/tests/test_data/duplicate_entries_same_depths.bam_readcount.vcf b/tests/test_data/duplicate_entries_same_depths.bam_readcount.vcf index 62178d1..0a1dc53 100644 --- a/tests/test_data/duplicate_entries_same_depths.bam_readcount.vcf +++ b/tests/test_data/duplicate_entries_same_depths.bam_readcount.vcf @@ -15,8 +15,6 @@ ##FILTER= ##FILTER= ##FORMAT= -##FORMAT= -##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= @@ -55,6 +53,8 @@ ##source=SelectVariants ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #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 diff --git a/tests/test_data/hom_ref.readcount.vcf b/tests/test_data/hom_ref.readcount.vcf index aa1bf2d..79aef9a 100644 --- a/tests/test_data/hom_ref.readcount.vcf +++ b/tests/test_data/hom_ref.readcount.vcf @@ -146,6 +146,8 @@ ##WildtypeProtein=The normal, non-mutated protein sequence ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #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:.:. diff --git a/tests/test_data/indel_mode.bam_readcount.vcf b/tests/test_data/indel_mode.bam_readcount.vcf index e7fe27b..c94f2a4 100644 --- a/tests/test_data/indel_mode.bam_readcount.vcf +++ b/tests/test_data/indel_mode.bam_readcount.vcf @@ -80,9 +80,11 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #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 diff --git a/tests/test_data/mnp.readcount.vcf.gz b/tests/test_data/mnp.readcount.vcf.gz index e65d612..eac3ed9 100644 Binary files a/tests/test_data/mnp.readcount.vcf.gz and b/tests/test_data/mnp.readcount.vcf.gz differ diff --git a/tests/test_data/multiple_samples.readcount.vcf b/tests/test_data/multiple_samples.readcount.vcf index 24f8a10..3c3a076 100644 --- a/tests/test_data/multiple_samples.readcount.vcf +++ b/tests/test_data/multiple_samples.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 H_NJ-HCC1395-HCC1396 -22 16202096 . C A,T . . CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T|||| GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD 0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0 0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.:.:. +22 16202096 . C A,T . . CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T|||| GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR 0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0 0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.:.:.:.:. diff --git a/tests/test_data/multiple_samples_second_alt.readcount.vcf b/tests/test_data/multiple_samples_second_alt.readcount.vcf index 37d9976..3edb89c 100644 --- a/tests/test_data/multiple_samples_second_alt.readcount.vcf +++ b/tests/test_data/multiple_samples_second_alt.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 H_NJ-HCC1395-HCC1396 -22 16202096 . C A,T . . CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T|||| GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD 0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.375,0.0:10,6,0 0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0 +22 16202096 . C A,T . . CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T|||| GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR 0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.375,0.0:10,6,0:6,5,0:4,1,0 0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0 diff --git a/tests/test_data/no_matching_readcount.readcount.vcf b/tests/test_data/no_matching_readcount.readcount.vcf index 45e0529..bb12ed4 100644 --- a/tests/test_data/no_matching_readcount.readcount.vcf +++ b/tests/test_data/no_matching_readcount.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 22 18644674 . 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:DP:AF:AD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0:0:0,0 diff --git a/tests/test_data/single_sample.dna.readcount.vcf b/tests/test_data/single_sample.dna.readcount.vcf index c6816d6..2042a27 100644 --- a/tests/test_data/single_sample.dna.readcount.vcf +++ b/tests/test_data/single_sample.dna.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 -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:DP:AF:AD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5 +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:DP:AF:AD:ADF:ADR 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2 diff --git a/tests/test_data/single_sample.rna.readcount.vcf b/tests/test_data/single_sample.rna.readcount.vcf index 274be46..8a79107 100644 --- a/tests/test_data/single_sample.rna.readcount.vcf +++ b/tests/test_data/single_sample.rna.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 -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:RDP:RAF:RAD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5 +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:RDP:RAF:RAD:RADF:RADR 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2 diff --git a/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf b/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf index a3ab8cb..5bd98fa 100644 --- a/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf +++ b/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf @@ -80,6 +80,8 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395 -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:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:AF 0/1:102,5:.:2:107:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0.04673 +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:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:AF:ADF:ADR 0/1:102,5:.:2:107:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0.04673:43,3:59,2 diff --git a/tests/test_data/snv_mode.bam_readcount.vcf b/tests/test_data/snv_mode.bam_readcount.vcf index 3c4ad9b..f863672 100644 --- a/tests/test_data/snv_mode.bam_readcount.vcf +++ b/tests/test_data/snv_mode.bam_readcount.vcf @@ -80,9 +80,11 @@ ##INFO= ##FORMAT= ##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= #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 0/1:76:13,9,28,26:36:2:12:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS 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 0/1:200:43,47,54,56:34:2:56:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS 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:AF 1/1:0,0:42:2:0:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60:0 -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:DP:AF:AD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5 +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:DP:AF:AD:ADF:ADR 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2 diff --git a/vatools/vcf_readcount_annotator.py b/vatools/vcf_readcount_annotator.py index ebfd7f8..d7f0473 100644 --- a/vatools/vcf_readcount_annotator.py +++ b/vatools/vcf_readcount_annotator.py @@ -46,11 +46,15 @@ def define_parser(): return parser def parse_brct_field(brcts): - parsed_brct = {} + counts = {} + forward_counts = {} + reverse_counts = {} for brct in brcts: - (base, count, rest) = brct.split(':', 2) - parsed_brct[base.upper()] = count - return parsed_brct + (base, count, avg_mapping_quality, avg_basequality, avg_se_mapping_quality, num_plus_strand, num_minus_strand, rest) = brct.split(':', 7) + counts[base.upper()] = count + forward_counts[base.upper()] = num_plus_strand + reverse_counts[base.upper()] = num_minus_strand + return counts, forward_counts, reverse_counts def parse_bam_readcount_file(args): coverage = {} @@ -62,8 +66,13 @@ def parse_bam_readcount_file(args): reference_base = row[2].upper() depth = row[3] brct = row[4:] - parsed_brct = parse_brct_field(brct) - parsed_brct['depth'] = depth + counts, forward_counts, reverse_counts = parse_brct_field(brct) + parsed_brct = { + 'counts': counts, + 'forward_counts': forward_counts, + 'reverse_counts': reverse_counts, + 'depth': depth + } if (chromosome, position, reference_base) in coverage and parsed_brct != coverage[(chromosome,position,reference_base)]: prev_brct = coverage[(chromosome, position, reference_base)] if prev_brct["depth"] == depth: @@ -167,17 +176,21 @@ def create_vcf_writer(args, vcf_reader): new_header = vcfpy.Header(samples = vcf_reader.header.samples) if args.data_type == 'DNA': for line in vcf_reader.header.lines: - if not (line.key == 'FORMAT' and line.id in ['DP', 'AD', 'AF']): + if not (line.key == 'FORMAT' and line.id in ['DP', 'AD', 'ADF', 'ADR','AF']): new_header.add_line(line) new_header.add_format_line(OrderedDict([('ID', 'DP'), ('Number', '1'), ('Type', 'Integer'), ('Description', 'Read depth')])) new_header.add_format_line(OrderedDict([('ID', 'AD'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'Allelic depths for the ref and alt alleles in the order listed')])) + new_header.add_format_line(OrderedDict([('ID', 'ADF'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'Allelic depths on the forward strand (high-quality bases)')])) + new_header.add_format_line(OrderedDict([('ID', 'ADR'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'Allelic depths on the reverse strand (high-quality bases)')])) new_header.add_format_line(OrderedDict([('ID', 'AF'), ('Number', 'A'), ('Type', 'Float'), ('Description', 'Variant-allele frequency for the alt alleles')])) if args.data_type == 'RNA': for line in vcf_reader.header.lines: - if not (line.key == 'FORMAT' and line.id in ['RDP', 'RAD', 'RAF']): + if not (line.key == 'FORMAT' and line.id in ['RDP', 'RAD', 'RADF', 'RADR', 'RAF']): new_header.add_line(line) new_header.add_format_line(OrderedDict([('ID', 'RDP'), ('Number', '1'), ('Type', 'Integer'), ('Description', 'RNA Read depth')])) new_header.add_format_line(OrderedDict([('ID', 'RAD'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'RNA Allelic depths for the ref and alt alleles in the order listed')])) + new_header.add_format_line(OrderedDict([('ID', 'RADF'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'RNA Allelic depths on the forward strand (high-quality bases)')])) + new_header.add_format_line(OrderedDict([('ID', 'RADR'), ('Number', 'R'), ('Type', 'Integer'), ('Description', 'RNA Allelic depths on the reverse strand (high-quality bases)')])) new_header.add_format_line(OrderedDict([('ID', 'RAF'), ('Number', 'A'), ('Type', 'Float'), ('Description', 'RNA Variant-allele frequency for the alt alleles')])) return vcfpy.Writer.from_path(output_file, new_header) @@ -197,10 +210,14 @@ def main(args_input = sys.argv[1:]): if args.data_type == 'DNA': depth_field = 'DP' count_field = 'AD' + forward_count_field = 'ADF' + reverse_count_field = 'ADR' frequency_field = 'AF' elif args.data_type == 'RNA': depth_field = 'RDP' count_field = 'RAD' + forward_count_field = 'RADF' + reverse_count_field = 'RADR' frequency_field = 'RAF' for entry in vcf_reader: @@ -216,7 +233,7 @@ def main(args_input = sys.argv[1:]): #from a single number to an array or else the writer will throw an error for sample in vcf_reader.header.samples.names: sample_data = entry.call_for_sample[sample].data - for field in [count_field, frequency_field]: + for field in [count_field, forward_count_field, reverse_count_field, frequency_field]: if field in sample_data and (not isinstance(sample_data[field], list)): sample_data[field] = [sample_data[field]] @@ -267,7 +284,7 @@ def main(args_input = sys.argv[1:]): write_depth(entry, sample_name, depth_field, depth) #If `depth` is the only key in this hash, then this must have - #been a duplicate bam-readcoutn entry where only the depths matched. + #been a duplicate bam-readcount entry where only the depths matched. #The only field to write is depth; frequency and count fields should not be written. if len(brct.keys()) == 1 and list(brct.keys())[0] == 'depth': vcf_writer.write_record(entry) @@ -282,35 +299,36 @@ def main(args_input = sys.argv[1:]): (bam_readcount_position, ref_base, var_base) = parse_to_bam_readcount(start, reference, alt, entry.POS) brct = read_counts.get((chromosome,bam_readcount_position,ref_base), None) if brct is not None: - if var_base not in brct: + if var_base not in brct['counts']: print("Warning: variant base {} is not present in the bam-readcount entry for variant {} {}. This might indicate that the bam-readcount file doesn't match the VCF.".format(var_base, chromosome, start)) vafs.append(0) else: - vafs.append(calculate_vaf(int(brct[var_base]), depth)) + vafs.append(calculate_vaf(int(brct['counts'][var_base]), depth)) else: vafs.append(0) entry.call_for_sample[sample_name].data[frequency_field] = vafs - #AD - ref, var1..varN counts - if count_field not in entry.FORMAT: - entry.FORMAT += [count_field] - (bam_readcount_position, ref_base, var_base) = parse_to_bam_readcount(start, reference, alts[0].serialize(), entry.POS) - brct = read_counts.get((chromosome,bam_readcount_position,ref_base), None) - ads = [] - ads.append(brct[ref_base]) - for alt in alts: - alt = alt.serialize() - (bam_readcount_position, ref_base, var_base) = parse_to_bam_readcount(start, reference, alt, entry.POS) + #AD/ADF/ADR - ref, var1..varN counts + for (field_name, value_name) in zip([count_field, forward_count_field, reverse_count_field], ['counts', 'forward_counts', 'reverse_counts']): + if field_name not in entry.FORMAT: + entry.FORMAT += [field_name] + (bam_readcount_position, ref_base, var_base) = parse_to_bam_readcount(start, reference, alts[0].serialize(), entry.POS) brct = read_counts.get((chromosome,bam_readcount_position,ref_base), None) - if brct is not None: - if var_base not in brct: - print("Warning: variant base {} is not present in the bam-readcount entry for variant {} {}. This might indicate that the bam-readcount file doesn't match the VCF.".format(var_base, chromosome, start)) - ads.append(0) + ads = [] + ads.append(brct[value_name][ref_base]) + for alt in alts: + alt = alt.serialize() + (bam_readcount_position, ref_base, var_base) = parse_to_bam_readcount(start, reference, alt, entry.POS) + brct = read_counts.get((chromosome,bam_readcount_position,ref_base), None) + if brct is not None: + if var_base not in brct[value_name]: + print("Warning: variant base {} is not present in the bam-readcount entry for variant {} {}. This might indicate that the bam-readcount file doesn't match the VCF.".format(var_base, chromosome, start)) + ads.append(0) + else: + ads.append(brct[value_name][var_base]) else: - ads.append(brct[var_base]) - else: - ads.append(0) - entry.call_for_sample[sample_name].data[count_field] = ads + ads.append(0) + entry.call_for_sample[sample_name].data[field_name] = ads vcf_writer.write_record(entry)