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update sv bothsides support parsing (#1111)
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-2
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4 files changed

+5
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‎v03_pipeline/lib/annotations/sv.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -122,7 +122,7 @@ def algorithms(ht: hl.Table, **_: Any) -> hl.Expression:
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def bothsides_support(ht: hl.Table, **_: Any) -> hl.Expression:
125-
return ht.filters.any(lambda x: x == 'BOTHSIDES_SUPPORT')
125+
return ht['info.BOTHSIDES_SUPPORT']
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def CN(mt: hl.MatrixTable, **_: Any) -> hl.Expression: # noqa: N802

‎v03_pipeline/lib/model/dataset_type.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -125,6 +125,7 @@ def row_fields(
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'info.AC': hl.tarray(hl.tint32),
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'info.AF': hl.tarray(hl.tfloat64),
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'info.ALGORITHMS': hl.tarray(hl.tstr),
128+
'info.BOTHSIDES_SUPPORT': hl.tbool,
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'info.AN': hl.tint32,
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'info.CHR2': hl.tstr,
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'info.CPX_INTERVALS': hl.tarray(hl.tstr),

‎v03_pipeline/var/test/callsets/sv_1.vcf

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
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##FORMAT=<ID=SR_GQ,Number=1,Type=Integer,Description="Split read genotype quality">
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##FORMAT=<ID=SR_GT,Number=1,Type=Integer,Description="Split-read genotype">
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##INFO=<ID=ALGORITHMS,Number=.,Type=String,Description="Source algorithms">
14+
##INFO=<ID=BOTHSIDES_SUPPORT,Number=0,Type=Flag,Description="Variant has read-level support for both sides of breakpoint">
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##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate">
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##INFO=<ID=CPX_INTERVALS,Number=.,Type=String,Description="Genomic intervals constituting complex variant.">
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##INFO=<ID=CPX_TYPE,Number=1,Type=String,Description="Class of complex variant.">
@@ -81,7 +82,7 @@ chr1 257666 DUP_chr1_5 N <DUP> 999 PASS ALGORITHMS=depth;CHR2=chr1;END=263666;EV
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chr1 413968 DEL_chr1_12 N <DEL> 999 PASS ALGORITHMS=depth;CHR2=chr1;END=428500;EVIDENCE=RD;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=OR4F29;SVLEN=14532;SVTYPE=DEL;AN=8;AC=1;AF=0.064926;N_BI_GENOS=2911;N_HOMREF=2538;N_HET=368;N_HOMALT=5;FREQ_HOMREF=0.871865;FREQ_HET=0.126417;FREQ_HOMALT=0.00171762;MALE_AN=2894;MALE_AC=172;MALE_AF=0.059433;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1278;MALE_N_HET=166;MALE_N_HOMALT=3;MALE_FREQ_HOMREF=0.883207;MALE_FREQ_HET=0.11472;MALE_FREQ_HOMALT=0.00207325;FEMALE_AN=2906;FEMALE_AC=205;FEMALE_AF=0.070544;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1250;FEMALE_N_HET=201;FEMALE_N_HOMALT=2;FEMALE_FREQ_HOMREF=0.860289;FEMALE_FREQ_HET=0.138334;FEMALE_FREQ_HOMALT=0.00137646 GT:EV:GQ:RD_CN:RD_GQ 0/0:RD:12:2:12 0/0:RD:0:2:0 0/1:RD:99:1:99 0/0:RD:2:2:2 0/0:RD:2:2:2
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chr1 789481 BND_chr1_9 N <BND> 999 PESR_GT_OVERDISPERSION;UNRESOLVED ALGORITHMS=manta;CHR2=chr1;END=789481;EVIDENCE=PE;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FBXO28,OR4F16;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;STRANDS=-+;SVLEN=223225007;SVTYPE=BND;UNRESOLVED_TYPE=SINGLE_ENDER_-+;AN=8;AC=7;AF=0.910684;N_BI_GENOS=2911;N_HOMREF=0;N_HET=520;N_HOMALT=2391;FREQ_HOMREF=0;FREQ_HET=0.178633;FREQ_HOMALT=0.821367;MALE_AN=2894;MALE_AC=2639;MALE_AF=0.911887;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=0;MALE_N_HET=255;MALE_N_HOMALT=1192;MALE_FREQ_HOMREF=0;MALE_FREQ_HET=0.176227;MALE_FREQ_HOMALT=0.823773;FEMALE_AN=2906;FEMALE_AC=2643;FEMALE_AF=0.909498;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=0;FEMALE_N_HET=263;FEMALE_N_HOMALT=1190;FEMALE_FREQ_HOMREF=0;FEMALE_FREQ_HET=0.181005;FEMALE_FREQ_HOMALT=0.818995 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 1/1:PE:59:59:2:99:0 1/1:PE:26:26:2:99:0 1/1:PE:39:39:2:99:0 0/1:PE:19:19:1:99:0 0/1:PE:19:19:1:99:0
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chr1 4228405 INS_chr1_65 N <INS:ME:ALU> 605 HIGH_SR_BACKGROUND ALGORITHMS=manta,melt;CHR2=chr1;END=4228448;EVIDENCE=SR;gnomAD_V2_SVID=gnomAD-SV_v2.1_INS_chr1_65;GNOMAD_V4.1_TRUTH_VID=gnomAD-SV_v3_BND_chr1_0001f5b7;gnomAD_V2_AF=0.068962998688221;gnomAD_V2_AC=224;gnomAD_V2_AN=3247;StrVCTVRE=0.1255;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=C1orf174;SVLEN=298;SVTYPE=INS;AN=8;AC=1;AF=0.10237;N_BI_GENOS=2911;N_HOMREF=2318;N_HET=590;N_HOMALT=3;FREQ_HOMREF=0.79629;FREQ_HET=0.202679;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=293;MALE_AF=0.101244;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1156;MALE_N_HET=289;MALE_N_HOMALT=2;MALE_FREQ_HOMREF=0.798894;MALE_FREQ_HET=0.199724;MALE_FREQ_HOMALT=0.00138217;FEMALE_AN=2906;FEMALE_AC=302;FEMALE_AF=0.103923;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1152;FEMALE_N_HET=300;FEMALE_N_HOMALT=1;FEMALE_FREQ_HOMREF=0.792842;FEMALE_FREQ_HET=0.206469;FEMALE_FREQ_HOMALT=0.000688231 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:62:99:0:62:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0
84-
chr1 6558902 CPX_chr1_22 N <CPX> 644 BOTHSIDES_SUPPORT;HIGH_SR_BACKGROUND ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP
85+
chr1 6558902 CPX_chr1_22 N <CPX> 644 HIGH_SR_BACKGROUND ALGORITHMS=manta;BOTHSIDES_SUPPORT;CHR2=chr1;CPX_INTERVALS=INV_chr1:6558902-6559723,DUP_chr1:6559655-6559723;CPX_TYPE=INVdup;END=6559723;EVIDENCE=PE,SR;PREDICTED_INTRONIC=TAS1R1;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=821;SVTYPE=CPX;AN=8;AC=2;AF=0.169873;N_BI_GENOS=2911;N_HOMREF=1925;N_HET=983;N_HOMALT=3;FREQ_HOMREF=0.661285;FREQ_HET=0.337685;FREQ_HOMALT=0.00103057;MALE_AN=2894;MALE_AC=497;MALE_AF=0.171735;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=950;MALE_N_HET=497;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.656531;MALE_FREQ_HET=0.343469;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=488;FEMALE_AF=0.167928;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=968;FEMALE_N_HET=482;FEMALE_N_HOMALT=3;FEMALE_FREQ_HOMREF=0.666208;FEMALE_FREQ_HET=0.331727;FEMALE_FREQ_HOMALT=0.00206469 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT:RD_CN:CONC_ST 0/0:PE,SR:99:99:0:99:0:2:EMPTY 0/1:PE,SR:57:0:0:57:1:2:TN,TP 0/1:PE,SR:0:0:1:99:0:2:FP,TN 0/0:PE,SR:99:99:0:0:0:3:FN 1/1:PE,SR:99:99:0:0:0:1:FP,TP
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chr1 16088760 CPX_chr1_41 N <CPX> 684 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:16088760-16088835,INV_chr1:16088760-16089601;CPX_TYPE=dupINV;END=16089601;EVIDENCE=PE,SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=FAM131C;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=841;SVTYPE=CPX;AN=8;AC=2;AF=0.218138;N_BI_GENOS=2911;N_HOMREF=1659;N_HET=1234;N_HOMALT=18;FREQ_HOMREF=0.569907;FREQ_HET=0.423909;FREQ_HOMALT=0.00618344;MALE_AN=2894;MALE_AC=635;MALE_AF=0.219419;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=818;MALE_N_HET=623;MALE_N_HOMALT=6;MALE_FREQ_HOMREF=0.565308;MALE_FREQ_HET=0.430546;MALE_FREQ_HOMALT=0.00414651;FEMALE_AN=2906;FEMALE_AC=629;FEMALE_AF=0.216449;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=836;FEMALE_N_HET=605;FEMALE_N_HOMALT=12;FEMALE_FREQ_HOMREF=0.575361;FEMALE_FREQ_HET=0.41638;FEMALE_FREQ_HOMALT=0.00825877 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:SR:52:0:0:52:1 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:62:0:0:62:1 0/1:SR:62:0:0:62:1
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chr1 17465707 INS_chr1_268 N <INS:ME:SVA> 263 HIGH_SR_BACKGROUND ALGORITHMS=melt;CHR2=chr1;END=17465723;EVIDENCE=SR;PREDICTED_INTERGENIC;PREDICTED_NEAREST_TSS=RCC2;PREDICTED_NONCODING_BREAKPOINT=Tommerup_TADanno;SVLEN=955;SVTYPE=INS;AN=8;AC=1;AF=0.004466;N_BI_GENOS=2911;N_HOMREF=2885;N_HET=26;N_HOMALT=0;FREQ_HOMREF=0.991068;FREQ_HET=0.00893164;FREQ_HOMALT=0;MALE_AN=2894;MALE_AC=14;MALE_AF=0.004838;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=1433;MALE_N_HET=14;MALE_N_HOMALT=0;MALE_FREQ_HOMREF=0.990325;MALE_FREQ_HET=0.00967519;MALE_FREQ_HOMALT=0;FEMALE_AN=2906;FEMALE_AC=11;FEMALE_AF=0.003785;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=1442;FEMALE_N_HET=11;FEMALE_N_HOMALT=0;FEMALE_FREQ_HOMREF=0.992429;FEMALE_FREQ_HET=0.00757054;FEMALE_FREQ_HOMALT=0 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/0:PE,SR:99:99:0:99:0 0/0:PE,SR:99:99:0:99:0 0/1:SR:0:99:0:0:1 0/0:PE,SR:99:99:0:2:0 0/0:PE,SR:99:99:0:2:0
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chr1 21427498 CPX_chr1_54 N <CPX> 733 PASS ALGORITHMS=manta;CHR2=chr1;CPX_INTERVALS=DUP_chr1:21427498-21427959,INV_chr1:21427498-21480073,DEL_chr1:21480073-21480419;CPX_TYPE=dupINVdel;END=21480419;EVIDENCE=PE;PREDICTED_LOF=NBPF3;PREDICTED_NONCODING_BREAKPOINT=DNase,Tommerup_TADanno;PREDICTED_NONCODING_SPAN=DNase;SVLEN=52921;SVTYPE=CPX;AN=8;AC=4;AF=0.499656;N_BI_GENOS=2911;N_HOMREF=51;N_HET=2811;N_HOMALT=49;FREQ_HOMREF=0.0175198;FREQ_HET=0.965648;FREQ_HOMALT=0.0168327;MALE_AN=2894;MALE_AC=1453;MALE_AF=0.502073;MALE_N_BI_GENOS=1447;MALE_N_HOMREF=19;MALE_N_HET=1403;MALE_N_HOMALT=25;MALE_FREQ_HOMREF=0.0131306;MALE_FREQ_HET=0.969592;MALE_FREQ_HOMALT=0.0172771;FEMALE_AN=2906;FEMALE_AC=1445;FEMALE_AF=0.497247;FEMALE_N_BI_GENOS=1453;FEMALE_N_HOMREF=32;FEMALE_N_HET=1397;FEMALE_N_HOMALT=24;FEMALE_FREQ_HOMREF=0.0220234;FEMALE_FREQ_HET=0.961459;FEMALE_FREQ_HOMALT=0.0165175 GT:EV:GQ:PE_GQ:PE_GT:SR_GQ:SR_GT 0/1:PE:93:93:1:99:0 0/1:PE:79:79:1:99:0 0/1:PE:33:33:1:6:0 0/1:PE,SR:39:39:1:99:0 0/1:PE,SR:39:39:1:99:0

‎v03_pipeline/var/test/callsets/sv_2.vcf

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
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##FORMAT=<ID=SR_GQ,Number=1,Type=Integer,Description="Split read genotype quality">
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##FORMAT=<ID=SR_GT,Number=1,Type=Integer,Description="Split-read genotype">
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##INFO=<ID=ALGORITHMS,Number=.,Type=String,Description="Source algorithms">
14+
##INFO=<ID=BOTHSIDES_SUPPORT,Number=0,Type=Flag,Description="Variant has read-level support for both sides of breakpoint">
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##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate">
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##INFO=<ID=CPX_INTERVALS,Number=.,Type=String,Description="Genomic intervals constituting complex variant.">
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##INFO=<ID=CPX_TYPE,Number=1,Type=String,Description="Class of complex variant.">

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