diff --git a/repo_utils/answer_key/collapse/inputintragt_collapsed.vcf b/repo_utils/answer_key/collapse/inputintragt_collapsed.vcf index 305885ed..32fc12b6 100644 --- a/repo_utils/answer_key/collapse/inputintragt_collapsed.vcf +++ b/repo_utils/answer_key/collapse/inputintragt_collapsed.vcf @@ -743,8 +743,8 @@ chr18 28783779 chr18-28783780-DEL-321;pbsv.DEL.493 CAAAAGAAAAGGCATTGGCCGGGCGCGGT chr18 28799448 chr18-28799449-INS-58 A ATATATATATATGTGTATATATATATATATGTGTATATATATATGTGTATATATATATG 4 . ID=chr18-28799449-INS-58;SVTYPE=INS;SVLEN=58;TIG_REGION=h1tg005703l:179702-179759;QUERY_STRAND=-;HOM_REF=0,13;HOM_TIG=0,25;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=245.0 GT:AD:DP:DR:DV:GQ:SAC:SUPP 1/1:1,5:6:.:5:13:1,0,3,2:7 chr18 28799493 chr18-28799494-INS-60 T TTGTGTATATATATATGTATATATATATGTGTGTATATTATATGATATATATATGTGTGTG 4 . ID=chr18-28799494-INS-60;SVTYPE=INS;SVLEN=60;TIG_REGION=h2tg005333l:179639-179698;QUERY_STRAND=-;HOM_REF=0,0;HOM_TIG=0,1;AC=1 GT:SUPP 0/1:1 chr18 28837163 chr18-28837164-INS-65;pbsv.INS.495 A AGGGGAGGGGAGGGGGAGGGGAGGGGGAGGGGAGGGAAGGGGAGGGGGAGGGGAGGGGGAGGGGAG 4 PASS ID=chr18-28837164-INS-65;SVTYPE=INS;SVLEN=65;TIG_REGION=h1tg005703l:141896-141960,h2tg005333l:141891-141955;QUERY_STRAND=-,-;HOM_REF=0,20;HOM_TIG=0,20;SVANN=TANDEM;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=246.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:5:13:7 -chr18 28883955 chr18-28883956-INS-82 T TATATCATATAATATCATATATATGATATATATCATATATATCATATATATGATAATATATGATATATATATCATATAATATC 4 . ID=chr18-28883956-INS-82;SVTYPE=INS;SVLEN=82;TIG_REGION=h2tg005333l:95009-95090;QUERY_STRAND=-;HOM_REF=0,4;HOM_TIG=0,4;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=247.0 GT:AD:DP:SAC:SUPP 1/1:0,4:4:0,0,3,1:5 -chr18 28883963 Sniffles2.INS.B2S11 G TCATATAATATCATATATATGATATATATCATATATATCATATATATGATAATATATGATATATATATCATATAATATCATATATAT 3 PASS PRECISE;SVTYPE=INS;SVLEN=87;SUPPORT=4;COVERAGE=4,4,4,4,3;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2 GT:GQ:DR:DV:SUPP 1/1:11:0:4:2 +chr18 28883955 chr18-28883956-INS-82 T TATATCATATAATATCATATATATGATATATATCATATATATCATATATATGATAATATATGATATATATATCATATAATATC 4 . ID=chr18-28883956-INS-82;SVTYPE=INS;SVLEN=82;TIG_REGION=h2tg005333l:95009-95090;QUERY_STRAND=-;HOM_REF=0,4;HOM_TIG=0,4;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=247.0 GT:AD:DP:SAC:SUPP 1/1:0,4:4:0,0,3,1:5 +chr18 28883961 chr18-28883962-INS-85 T TCATATAATATCATATATATGATATATATCATATATATCATATATATGATATTATATGATATATATATCATATAATATCATATATA 4 . ID=chr18-28883962-INS-85;SVTYPE=INS;SVLEN=85;TIG_REGION=h1tg005703l:95004-95088;QUERY_STRAND=-;HOM_REF=0,0;HOM_TIG=0,0;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=247.1 GT:DR:DV:GQ:SUPP 1/1:.:4:11:3 chr18 29394582 pbsv.DEL.497 GAAAAAGAAAGAAAGAAAGAAAGAA G 2 PASS SVTYPE=DEL;SVLEN=-24;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,10:10:0,0,3,7:4 chr18 29505721 pbsv.INS.DUP.498 T TTTTTTTTTTTTTTTTTTT 0 PASS SVTYPE=INS;SVLEN=18;AC=2 GT:AD:DP:SAC:SUPP 1/1:1,5:6:0,1,2,3:4 chr18 29511688 pbsv.INS.499 T TTTTATATATAATTTATATTTATATAA 2 PASS SVTYPE=INS;SVLEN=26;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,4:4:0,0,1,3:4 @@ -1567,7 +1567,8 @@ chr18 74425098 chr18-74425099-DEL-65 TTCCCGTCAGGAAGTCAGTCAGTTTCCCGTCAGGAAGTCAGTC chr18 74425132 chr18-74425133-DEL-88;pbsv.DEL.1205 AAGTCAGTCAGTTTCCCATCAGGAAGTCAGTCTCCCATCAGGAAGTCAGTCAGTTTCCCATCAGGAAGTCAGTTTCCCATCAGGAAGTC A 4 PASS ID=chr18-74425133-DEL-88;SVTYPE=DEL;SVLEN=-88;TIG_REGION=h1tg001608l:151999-151999;QUERY_STRAND=-;HOM_REF=0,7;HOM_TIG=0,7;SVANN=TANDEM;AC=3 GT:AD:DP:SAC:SUPP 1/1:0,11:11:0,0,4,7:5 chr18 74458604 pbsv.INS.DUP.1206 G GGGTTTGGGTGTCACTCAATCAACAGC 0 PASS SVTYPE=INS;SVLEN=26;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,5:5:0,0,3,2:4 chr18 74485193 chr18-74485194-DEL-340;pbsv.DEL.1207 TTCCATGATGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCAGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC T 4 PASS ID=chr18-74485194-DEL-340;SVTYPE=DEL;SVLEN=-340;TIG_REGION=h1tg001608l:91978-91978,h2tg010301l:28754-28754;QUERY_STRAND=-,-;HOM_REF=0,14;HOM_TIG=0,14;SVANN=ALU;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=505.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:10:27:7 -chr18 74503904 chr18-74503905-INS-54;pbsv.INS.1208 A ACACACGCAGCCACACTGCCGCTGGGACAAATGAGGGGCGTCAGGCCATACACTG 4 PASS ID=chr18-74503905-INS-54;SVTYPE=INS;SVLEN=54;TIG_REGION=h1tg001608l:73543-73596;QUERY_STRAND=-;HOM_REF=0,126;HOM_TIG=0,126;SVANN=TANDEM;AC=3;NumCollapsed=2;NumConsolidated=2;CollapseId=506.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:6:16:7 +chr18 74503904 chr18-74503905-INS-54;pbsv.INS.1208 A ACACACGCAGCCACACTGCCGCTGGGACAAATGAGGGGCGTCAGGCCATACACTG 4 PASS ID=chr18-74503905-INS-54;SVTYPE=INS;SVLEN=54;TIG_REGION=h1tg001608l:73543-73596;QUERY_STRAND=-;HOM_REF=0,126;HOM_TIG=0,126;SVANN=TANDEM;AC=3;NumCollapsed=1;NumConsolidated=1;CollapseId=506.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:6:16:7 +chr18 74503904 chr18-74503905-INS-54.1 A ACACACGCAGCCACACTGCCGCTGGGACAAATGATGGGCGTCAGGCCATACACTG 4 . ID=chr18-74503905-INS-54.1;SVTYPE=INS;SVLEN=54;TIG_REGION=h2tg010301l:10313-10366;QUERY_STRAND=-;HOM_REF=0,33;HOM_TIG=0,33;AC=1 GT:SUPP 0/1:1 chr18 74514629 pbsv.INS.1209 G GGATGTAAGTTCCGCAGGCTGTGGGTTTATGCGGTACA 2 PASS SVTYPE=INS;SVLEN=37;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:1,5:6:1,0,3,2:4 chr18 74573430 pbsv.INS.1210 A ATCCATTCATCCATCCATCCATCTATCTATGTA 2 PASS SVTYPE=INS;SVLEN=32;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:7,3:10:3,4,1,2:4 chr18 74617096 chr18-74617097-INS-1997 A ACACACATCCATATCCGTACACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACGCATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCATACACCACACACATCTATATCCACACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCATACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACACACCACACACATCCATATCCATGCTCCACACACATCTATATCCACACACATCCATATCCACACACATCCATATCCACACACCACATACATCCATATCCACGCACATCCATATCCACATGCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATTCATATCCATACACCACACACACCCATATCCACACACCATACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCGATATCCACGTACATCCATATCCACGCACCACACACATCCATATCCATGCACATCCATATCCACACACATCCATATCCACTCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATGTCCACACACATCCATATCCACACACCACACACATCCATATTCACACACATCCATATCCGCACACCACACACATCCATATTCACACACATCCATATCCACGCACATCCATATCTATGCACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCGACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACC 4 . ID=chr18-74617097-INS-1997;SVTYPE=INS;SVLEN=1997;TIG_REGION=h2tg009567l:102415-104411;QUERY_STRAND=+;HOM_REF=0,0;HOM_TIG=0,0;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=507.0 GT:AD:DP:DR:DV:GQ:SAC:SUPP 0/1:2,4:6:.:4:11:1,1,1,3:7 @@ -1656,7 +1657,8 @@ chr18 77029228 pbsv.DEL.1271 GCGAAACCCCGGCTCCACCAAAAAAATA G 2 PASS SVTYPE=DEL;SV chr18 77036952 pbsv.DEL.1272 TTGGAGACTGAGCTGAGCAAGTGCTGGTCACGTTT T 2 PASS SVTYPE=DEL;SVLEN=-34;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,11:11:0,0,4,7:4 chr18 77044912 pbsv.INS.1273 T TAAGAAAATGTGAGTCTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGCCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2 PASS SVTYPE=INS;SVLEN=343;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:5,6:11:2,3,2,4:4 chr18 77044931 chr18-77044932-INS-325 G GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGCCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4 . ID=chr18-77044932-INS-325;SVTYPE=INS;SVLEN=325;TIG_REGION=h1tg014962l:55578-55902;QUERY_STRAND=+;HOM_REF=0,0;HOM_TIG=0,0;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=533.0 GT:DR:DV:GQ:SUPP 0/1:5:6:33:3 -chr18 77045365 chr18-77045366-INS-87;pbsv.INS.1275 T TTGACCCGCTGCAGCAGCACCTGGCTGCACCAGGTCAGGGTCTCTGGAGCCCGGCTGCCAGCAGAGACATTTGCATGCGTCTCTGGAC 4 PASS ID=chr18-77045366-INS-87;SVTYPE=INS;SVLEN=87;TIG_REGION=h1tg014962l:56341-56427;QUERY_STRAND=+;HOM_REF=0,22;HOM_TIG=0,22;SVANN=TANDEM;AC=2;NumCollapsed=2;NumConsolidated=3;CollapseId=533.1 GT:AD:DP:SAC:DR:DV:GQ:SUPP 0/1:6,5:11:2,4,2,3:.:11:30:7 +chr18 77045365 chr18-77045366-INS-87;pbsv.INS.1275 T TTGACCCGCTGCAGCAGCACCTGGCTGCACCAGGTCAGGGTCTCTGGAGCCCGGCTGCCAGCAGAGACATTTGCATGCGTCTCTGGAC 4 PASS ID=chr18-77045366-INS-87;SVTYPE=INS;SVLEN=87;TIG_REGION=h1tg014962l:56341-56427;QUERY_STRAND=+;HOM_REF=0,22;HOM_TIG=0,22;SVANN=TANDEM;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=533.1 GT:AD:DP:SAC:DR:DV:GQ:SUPP 0/1:.,.:.:.:.:11:30:7 +chr18 77045365 chr18-77045366-INS-87.1;pbsv.INS.1274 T TTGACCCGCTGCAGCAGCACCTGGCTGCACCAGGTCAGGGTCTCTGGAGCCTGGCTGCCAGCAGAGACATTTGCATGCGTCTCTGGAC 4 PASS ID=chr18-77045366-INS-87.1;SVTYPE=INS;SVLEN=87;TIG_REGION=h2tg018293l:94840-94926;QUERY_STRAND=-;HOM_REF=0,22;HOM_TIG=0,22;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 0/1:6,5:11:2,4,2,3:5 chr18 77057814 chr18-77057815-DEL-301;pbsv.DEL.1276 GGCGGGGAGTGTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTTTTTTTAATAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTGTCGATCTCCTGACCTCGTGTTCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA G 4 PASS ID=chr18-77057815-DEL-301;SVTYPE=DEL;SVLEN=-301;TIG_REGION=h1tg014962l:68886-68886,h2tg018293l:82368-82368;QUERY_STRAND=+,-;HOM_REF=0,16;HOM_TIG=0,16;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=534.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:8:22:7 chr18 77081813 pbsv.INS.1277 C CATATATACACACACACACATATATATACACACACT 2 PASS SVTYPE=INS;SVLEN=35;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:3,3:6:2,1,2,1:4 chr18 77082732 chr18-77082733-INS-144;pbsv.INS.1278 T TGAGGAATCCTTCCTCCCTGCAGCAGCTGGCTGTCATAGGTGGTCTAGGGAACGCCATGTGGCTCAGAAGGACGAGGAATCCTTCCTCCCTGCTGCAGCTAGCTGTCATAGGTGGTCTAGGGAACGCCATGTGGCTCAGAAGGAC 4 PASS ID=chr18-77082733-INS-144;SVTYPE=INS;SVLEN=144;TIG_REGION=h2tg018293l:57580-57723;QUERY_STRAND=-;HOM_REF=0,26;HOM_TIG=0,26;SVANN=TANDEM;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=535.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 0/1:.,.:.:.:2:3:11:7 @@ -1701,10 +1703,11 @@ chr18 77926771 Sniffles2.DEL.388S11 TGATTAATTATATATTAATCATACATTATATCATATAATCATAT chr18 77926815 chr18-77926816-DEL-60 AATATTATATATATATATTATATATAATATATATGATATATATATAATATATCATATATAT A 4 . ID=chr18-77926816-DEL-60;SVTYPE=DEL;SVLEN=-60;TIG_REGION=h1tg024234l:3468-3468,h2tg001461l:205973-205973;QUERY_STRAND=+,-;HOM_REF=0,0;HOM_TIG=0,0;AC=2 GT:SUPP 1/1:1 chr18 77927154 pbsv.INS.1309 T TTATATATAAAATATGTTGCATTTTATATATTTA 2 PASS SVTYPE=INS;SVLEN=33;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:1,4:5:0,1,3,1:4 chr18 77928821 pbsv.INS.1310 T TTTAGAATATTTATTCTAATACTATAGAATATTAAATAT 2 PASS SVTYPE=INS;SVLEN=38;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,5:5:0,0,3,2:4 -chr18 77957441 chr18-77957442-INS-100 A ACAACTCCAACACCACCACCACCAGCACCACCAATAACACTATCACCCCAACAACTCCAACACCACCACCAACACCAGCACCACCAATAACACTATCACCC 4 . ID=chr18-77957442-INS-100;SVTYPE=INS;SVLEN=100;TIG_REGION=h1tg024234l:33870-33969;QUERY_STRAND=+;HOM_REF=0,21;HOM_TIG=0,21;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=547.0 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 -chr18 77957621 chr18-77957622-INS-256 C CCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCCAAAAACACTACCACCCCAACAACTCCAACACCACCACCACCAGCACCCCCCAATAACACTATCACCCCAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACCGCCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCA 4 . ID=chr18-77957622-INS-256;SVTYPE=INS;SVLEN=256;TIG_REGION=h1tg024234l:34148-34403,h2tg001461l:174846-175100;QUERY_STRAND=+,-;HOM_REF=0,6;HOM_TIG=0,6;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=547.1 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 +chr18 77957441 chr18-77957442-INS-100 A ACAACTCCAACACCACCACCACCAGCACCACCAATAACACTATCACCCCAACAACTCCAACACCACCACCAACACCAGCACCACCAATAACACTATCACCC 4 . ID=chr18-77957442-INS-100;SVTYPE=INS;SVLEN=100;TIG_REGION=h1tg024234l:33870-33969;QUERY_STRAND=+;HOM_REF=0,21;HOM_TIG=0,21;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=547.0 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 +chr18 77957441 chr18-77957442-INS-96 A ACTCCAACACCACCACCACGAGCACCCCAAAAACACTATCACCCCAACAACTCCAACACCACCACCAACACCAGCACCACCAATAACACTATCACCC 4 . ID=chr18-77957442-INS-96;SVTYPE=INS;SVLEN=96;TIG_REGION=h2tg001461l:175280-175375;QUERY_STRAND=-;HOM_REF=0,1;HOM_TIG=0,1;AC=1 GT:SUPP 0/1:1 +chr18 77957621 chr18-77957622-INS-256 C CCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCCAAAAACACTACCACCCCAACAACTCCAACACCACCACCACCAGCACCCCCCAATAACACTATCACCCCAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACCGCCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCA 4 . ID=chr18-77957622-INS-256;SVTYPE=INS;SVLEN=256;TIG_REGION=h1tg024234l:34148-34403,h2tg001461l:174846-175100;QUERY_STRAND=+,-;HOM_REF=0,6;HOM_TIG=0,6;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=547.2 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 chr18 77957817 pbsv.INS.1311 C CCACCACCAGCACCCCCAATAACACTATCACCCCAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACCGCCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCAAAAACACTATCACCCCAACAACTCCAACACCAACGCCAACACCAGCAGCCCAATAACACTATCACCCCAACAACCCCAACACCACCGCCAACACCAGCACCACCAATATCACTATCATCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCAAAAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCGCAAAAACACTATCACCCCAACAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCAC 2 PASS SVTYPE=INS;SVLEN=461;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,5:5:0,0,2,3:4 -chr18 77958110 chr18-77958111-INS-103 T TCAACAACTCCAACCCCACTGCCAACACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACAACCACCACGAGCACCCCCAATAACACTATCACCC 4 . ID=chr18-77958111-INS-103;SVTYPE=INS;SVLEN=103;TIG_REGION=h1tg024234l:34892-34994,h2tg001461l:174254-174356;QUERY_STRAND=+,-;HOM_REF=0,68;HOM_TIG=0,68;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=547.2 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 +chr18 77958110 chr18-77958111-INS-103 T TCAACAACTCCAACCCCACTGCCAACACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACAACCACCACGAGCACCCCCAATAACACTATCACCC 4 . ID=chr18-77958111-INS-103;SVTYPE=INS;SVLEN=103;TIG_REGION=h1tg024234l:34892-34994,h2tg001461l:174254-174356;QUERY_STRAND=+,-;HOM_REF=0,68;HOM_TIG=0,68;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=547.3 GT:DR:DV:GQ:SUPP 1/1:.:5:13:3 chr18 77969362 pbsv.INS.1312 G GTGGCTGTCTTCCCTCCCAGGGGCAGATGCTGG 2 PASS SVTYPE=INS;SVLEN=32;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:0,6:6:0,0,4,2:4 chr18 78010174 chr18-78010175-INS-904;pbsv.INS.1313 A AGTGGTGGTGATAGTGATGATGATGGTGGTGATGGTGTTGCTAGTGGTAATGGCAGTGATAATGATGCTGGTGGTGGTGATGGTGGTGATGGTAGTGATGATGATGGTGGTGATGGTGTTAGTGTTGGTAGTGGGAATGGTAGTGATGGTGGTGGTGGTGGCGATGGTGCTGGTGGTGATGAGAATGGTTGTGTTGGTGGTGGCAGTAGTGATGGTGATGACTGTAGTGGTGATGGTGGTGGTGATAGTGATGGTGGTGGTGGTGGTGGTGATGGTGGTGATGATGGTGATGGTGATAGTGGTGGTGATAGTGGTGGTAGTGACAGTGGTAGTGATGGTGGCAGTAGTGATGGTGATGATGGTGTTGGTGATGGTGGTGGTGATGGTGGTGATGATGGTGATGGTGATAGTGGTGGTGATGGTGGTGGTAGTGACAGTGGTAGTGATGGTGGCAGTAGTGATGGTGATGATGGTGTTGGTGATGGTGGTGGTGGTGGTGATGATGGTGATGGTGATGATGATGGTGGTGGTGGTGAGGATGGTGATAGTGAGGATGATGGTGGTGGTGGTGATGGTGGTGGTGATAGTGATGATGGTGTTGGTGATGGTGATGGTGATGATGTTGATTGTGATGGTGGTGGTGGTGATAGTGATATGGTGATGGTGGTGGTGAAGGTGATGGTGATGGTGGTGGTGGTGGTGGTGAGGATGGTGATAGTGAGGATGATGGTGGTGGTGGTGGTGATGGTGGTGGTGGAGGTGGTGATAGTGATGATGGTGTTGGTGATGGTGATGGTGATGATGGTGATGATGTTGACTGTGATGGTGGTGGTGGTGATGGTGATATGGTGATGGTGGTGGTGATGGTGATGATGGTGATGGTGATGATGTTGACTGTGATGGTG 4 PASS ID=chr18-78010175-INS-904;SVTYPE=INS;SVLEN=904;TIG_REGION=h1tg010337l:21630-22533,h2tg001461l:121258-122161;QUERY_STRAND=+,-;HOM_REF=0,11;HOM_TIG=0,11;SVANN=TANDEM;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=548.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:9:25:7 chr18 78041169 chr18-78041170-DEL-52 ATTACAATTTACTTGGTTTGGGGGCTTAGATTCACAGATGGTTTCTTTCGCTT A 4 . ID=chr18-78041170-DEL-52;SVTYPE=DEL;SVLEN=-52;TIG_REGION=h2tg001461l:90200-90200;QUERY_STRAND=-;HOM_REF=0,1;HOM_TIG=0,1;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=549.0 GT:AD:DP:DR:DV:GQ:SAC:SUPP 0/1:5,4:9:5:4:26:4,1,3,1:7 @@ -1759,12 +1762,14 @@ chr18 78504365 chr18-78504366-DEL-51;pbsv.DEL.1350 CCCTGAGGATGCCAGCCCGACAGAGCACG chr18 78513047 chr18-78513048-INS-51;pbsv.INS.1351 C CCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGAT 4 PASS ID=chr18-78513048-INS-51;SVTYPE=INS;SVLEN=51;TIG_REGION=h1tg002297l:50094-50144,h2tg008125l:3992-4042;QUERY_STRAND=+,-;HOM_REF=0,85;HOM_TIG=0,85;SVANN=TANDEM;AC=3;NumCollapsed=1;NumConsolidated=1;CollapseId=572.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 0/1:.,.:.:.:1:5:3:7 chr18 78513098 Sniffles2.INS.1AAS11 T GTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCCAAGT 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=257;SUPPORT=2;COVERAGE=5,5,6,7,7;STRAND=-;AF=0.333;STDEV_LEN=37.477;STDEV_POS=10.607;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:8:4:2:2 chr18 78513230 pbsv.SPLIT.DUP.1352 C CCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAACCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCC 0 PASS SVTYPE=INS;SVLEN=1683;NotFullySpanned;AC=1 GT:AD:DP:SAC:SUPP 0/1:7,1:8:1,6,0,1:4 -chr18 78513435 pbsv.INS.DUP.1353 C CAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAACCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACC 0 PASS SVTYPE=INS;SVLEN=1477;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=572.9 GT:AD:DP:SAC:SUPP 0/1:7,2:9:0,7,1,1:4 +chr18 78513435 pbsv.INS.DUP.1353 C CAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAACCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACC 0 PASS SVTYPE=INS;SVLEN=1477;AC=1 GT:AD:DP:SAC:SUPP 0/1:7,1:8:0,7,1,0:4 +chr18 78513495 pbsv.SPLIT.DUP.1354 G GCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAACCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCC 0 PASS SVTYPE=INS;SVLEN=1418;AC=1 GT:AD:DP:SAC:SUPP 0/1:7,2:9:0,7,1,1:4 chr18 78513842 chr18-78513843-INS-153 G GCAAGAGTCAGCCTATCTAGACCTACTACAGTGGGTCAGCAGACACTACCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCC 4 . ID=chr18-78513843-INS-153;SVTYPE=INS;SVLEN=153;TIG_REGION=h2tg008125l:3045-3197;QUERY_STRAND=-;HOM_REF=0,27;HOM_TIG=0,27;AC=1 GT:SUPP 0/1:1 chr18 78513929 Sniffles2.INS.1ACS11 T GTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGT 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=53;SUPPORT=3;COVERAGE=7,9,9,9,9;STRAND=+-;AF=0.333;STDEV_LEN=1.155;STDEV_POS=35.557;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:13:6:3:2 chr18 78514043 chr18-78514044-INS-102 G GCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTA 4 . ID=chr18-78514044-INS-102;SVTYPE=INS;SVLEN=102;TIG_REGION=h2tg008125l:2742-2843;QUERY_STRAND=-;HOM_REF=0,18;HOM_TIG=0,50;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=572.2 GT:DR:DV:GQ:SUPP 0/1:5:2:6:3 -chr18 78514114 Sniffles2.INS.1ADS11 T TAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGGTCAGCCTATC 3 PASS PRECISE;SVTYPE=INS;SVLEN=52;SUPPORT=3;COVERAGE=7,9,9,9,4;STRAND=-;AF=0.333;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=572.6 GT:GQ:DR:DV:SUPP 0/1:14:2:2:2 +chr18 78514114 Sniffles2.INS.1ADS11 T TAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGGTCAGCCTATC 3 PASS PRECISE;SVTYPE=INS;SVLEN=52;SUPPORT=3;COVERAGE=7,9,9,9,4;STRAND=-;AF=0.333;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:13:6:3:2 chr18 78514220 chr18-78514221-INS-2040 C CCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTT 4 . ID=chr18-78514221-INS-2040;SVTYPE=INS;SVLEN=2040;TIG_REGION=h1tg002297l:51320-53359;QUERY_STRAND=+;HOM_REF=0,29;HOM_TIG=0,29;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=572.3 GT:AD:DP:SAC:SUPP 0/1:4,2:6:2,2,0,2:5 +chr18 78514605 Sniffles2.INS.1AFS11 C CCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTG 3 PASS PRECISE;SVTYPE=INS;SVLEN=51;SUPPORT=2;COVERAGE=9,8,4,4,4;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:14:2:2:2 chr18 78514884 Sniffles2.INS.1B3S11 C CTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGCACTACCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATTTAGAC 3 PASS PRECISE;SVTYPE=INS;SVLEN=410;SUPPORT=2;COVERAGE=9,4,4,4,4;STRAND=-;AF=0.5;STDEV_LEN=2.121;STDEV_POS=0;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:14:2:2:2 chr18 78516935 chr18-78516936-INS-164 T TGTTTTCCAAGTTGGACTCTGTAAAGTCCCAGAAATCCACAAGATTTTCATTCCTTATATTCATGTTGGACACTGTTACTGAAGAACCACGTTCCTTTTATCCTGGAGGAAAGAGGACGGGTCATGTGGCTGTACCTGCACCTCATCGCCCTTGGCCCAACCCCA 4 . ID=chr18-78516936-INS-164;SVTYPE=INS;SVLEN=164;TIG_REGION=h1tg002297l:56074-56237;QUERY_STRAND=+;HOM_REF=0,168;HOM_TIG=0,168;AC=1 GT:SUPP 1/0:1 chr18 78517726 chr18-78517727-INS-82 T TTGTCTCGGAAGCGGGGCCCTCAGGCACAGAGCCCGCCGCCTTGTCCCGGAAGCGGGGCCGTCAGGCACAGAGCCCGGCGCCC 4 . ID=chr18-78517727-INS-82;SVTYPE=INS;SVLEN=82;TIG_REGION=h1tg002297l:57070-57151;QUERY_STRAND=+;HOM_REF=0,4;HOM_TIG=0,59;AC=1 GT:SUPP 1/0:1 @@ -1843,8 +1848,8 @@ chr18 79033224 Sniffles2.INS.1D1S11 C CAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGT chr18 79033282 Sniffles2.INS.1D0S11 A ACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCACA 3 GT PRECISE;SVTYPE=INS;SVLEN=297;SUPPORT=2;COVERAGE=8,8,8,8,8;STRAND=-;AF=0.25;STDEV_LEN=0.707;STDEV_POS=7.778;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:3:6:2:2 chr18 79033353 pbsv.INS.1398 A ACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTTCTCATGGCTGCCATGTCTCATAGCCTTCCA 2 PASS SVTYPE=INS;SVLEN=1036;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:5,4:9:2,3,0,4:4 chr18 79033650 chr18-79033651-INS-148 T TGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCAC 4 . ID=chr18-79033651-INS-148;SVTYPE=INS;SVLEN=148;TIG_REGION=h2tg020617l:80478-80625;QUERY_STRAND=+;HOM_REF=0,73;HOM_TIG=0,73;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=600.1 GT:DR:DV:GQ:SUPP 0/1:6:2:3:3 -chr18 79034094 chr18-79034095-INS-74 T TGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTTCTCATGGCTGCCATGTCTCATAGCCTTCCAC 4 . ID=chr18-79034095-INS-74;SVTYPE=INS;SVLEN=74;TIG_REGION=h2tg020617l:81070-81143;QUERY_STRAND=+;HOM_REF=0,42;HOM_TIG=0,42;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=600.2 GT:SUPP 0/1:1 -chr18 79034325 Sniffles2.INS.1D2S11 C CCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCAC 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=74;SUPPORT=3;COVERAGE=8,8,8,8,8;STRAND=+-;AF=0.375;STDEV_LEN=1;STDEV_POS=65.241;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:16:5:3:2 +chr18 79034094 chr18-79034095-INS-74 T TGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTTCTCATGGCTGCCATGTCTCATAGCCTTCCAC 4 . ID=chr18-79034095-INS-74;SVTYPE=INS;SVLEN=74;TIG_REGION=h2tg020617l:81070-81143;QUERY_STRAND=+;HOM_REF=0,42;HOM_TIG=0,42;AC=1 GT:SUPP 0/1:1 +chr18 79034317 chr18-79034318-INS-74 A AACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATG 4 . ID=chr18-79034318-INS-74;SVTYPE=INS;SVLEN=74;TIG_REGION=h2tg020617l:81367-81440;QUERY_STRAND=+;HOM_REF=0,62;HOM_TIG=0,72;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=600.3 GT:DR:DV:GQ:SUPP 0/1:5:3:16:3 chr18 79034438 chr18-79034439-DEL-740 TGGCTGCCATATCTCAGAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATATCTCAGAGCCTTCCACAACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATATCTCAGAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAA T 4 . ID=chr18-79034439-DEL-740;SVTYPE=DEL;SVLEN=-740;TIG_REGION=h1tg002297l:576027-576027;QUERY_STRAND=+;HOM_REF=0,9;HOM_TIG=0,9;AC=1 GT:SUPP 1/0:1 chr18 79035860 chr18-79035861-INS-148 T TAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATGTCTCAGAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAG 4 . ID=chr18-79035861-INS-148;SVTYPE=INS;SVLEN=148;TIG_REGION=h2tg020617l:82984-83131;QUERY_STRAND=+;HOM_REF=0,9;HOM_TIG=0,57;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=601.0 GT:AD:DP:SAC:SUPP 0/1:7,2:9:2,5,0,2:5 chr18 79036315 chr18-79036316-INS-296 G GACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAGAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATATCTCAGAGCCTTCCACA 4 . ID=chr18-79036316-INS-296;SVTYPE=INS;SVLEN=296;TIG_REGION=h2tg020617l:83587-83882;QUERY_STRAND=+;HOM_REF=0,62;HOM_TIG=0,62;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=601.1 GT:DR:DV:GQ:SUPP 0/1:4:3:18:3 @@ -1871,7 +1876,8 @@ chr18 79336167 chr18-79336168-INS-310 G GTGCCCTCCCTGGCACCAGGCGCTCCCCTCGCCCGTCCCC chr18 79339254 pbsv.INS.1412 A ATGTCATGATCACAGTAGGAAGTG 2 PASS SVTYPE=INS;SVLEN=23;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:3,6:9:2,1,2,4:4 chr18 79341279 chr18-79341280-DEL-122;pbsv.DEL.1413 TCTGTGTTGCCGACACACCATTTAGTTGTGGTTGGATGTGTGTAGCGTGACCTCGTCGAAGTCTGTGTTGCCGACACACCATTTAGTTGTGGTTGGATGTGTGTAGCGTGACCTCGTTGAAGC T 4 PASS ID=chr18-79341280-DEL-122;SVTYPE=DEL;SVLEN=-122;TIG_REGION=h1tg015446l:143847-143847,h2tg014906l:143847-143847;QUERY_STRAND=+,+;HOM_REF=0,55;HOM_TIG=0,55;SVANN=TANDEM;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=610.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:7:19:7 chr18 79346415 chr18-79346416-DEL-139;pbsv.DEL.1414 TGGTCAGCGCACGTCAGCACGTGCTCAGCGCACAGTCAGCACACATTCGGCACACATTTAGCACACTACATGCTTGGCACACACTCAGCGCACCTCAGCATGTGTTCAGTGCACAGTCAGCACACACTCGGCACACACTC T 4 PASS ID=chr18-79346416-DEL-139;SVTYPE=DEL;SVLEN=-139;TIG_REGION=h1tg015243l:135116-135116,h2tg021222l:11330-11330;QUERY_STRAND=-,+;HOM_REF=0,166;HOM_TIG=0,166;SVANN=TANDEM;AC=4;NumCollapsed=1;NumConsolidated=1;CollapseId=611.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 1/1:.,.:.:.:.:7:19:7 -chr18 79357382 pbsv.DEL.1415 CCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGT C 2 PASS SVTYPE=DEL;SVLEN=-436;SVANN=TANDEM;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=612.9 GT:AD:DP:SAC:SUPP 0/1:3,1:4:1,2,0,1:4 +chr18 79357382 pbsv.DEL.1415 CCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGT C 2 PASS SVTYPE=DEL;SVLEN=-436;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:3,1:4:1,2,0,1:4 +chr18 79357396 pbsv.DEL.1416 GTCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTG G 2 PASS SVTYPE=DEL;SVLEN=-436;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:3,1:4:1,2,0,1:4 chr18 79357460 chr18-79357461-INS-170 T TCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTAGAGGTGTCCGTGTGAGGGACC 4 . ID=chr18-79357461-INS-170;SVTYPE=INS;SVLEN=170;TIG_REGION=h1tg015243l:124064-124233;QUERY_STRAND=-;HOM_REF=0,14;HOM_TIG=0,14;AC=1 GT:SUPP 1/0:1 chr18 79357515 pbsv.INS.1417 G GGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTAGAGGTGTCCGTGTGAGGGACCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGATGCTCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGAACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGA 2 PASS SVTYPE=INS;SVLEN=1005;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:3,2:5:1,2,1,1:4 chr18 79357633 Sniffles2.INS.1E9S11 C CTGGGTCTGGAGGTGTCCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCT 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=155;SUPPORT=3;COVERAGE=4,4,4,4,4;STRAND=+-;AF=0.75;STDEV_LEN=31.757;STDEV_POS=150.696;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:1:1:3:2 @@ -1920,10 +1926,11 @@ chr18 79585703 pbsv.DEL.1440 GCACACTCCCACACCCCATGCTCCCACTGTGTCCCCA G 2 PASS SVTY chr18 79610384 pbsv.DEL.1441 CTGAGCCACCCCAGGCAGGCTGAGCCCCCGCCTC C 2 PASS SVTYPE=DEL;SVLEN=-33;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:4,3:7:3,1,2,1:4 chr18 79617314 chr18-79617315-INS-274;pbsv.INS.1442 C CCCCCGGGACCCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCGCCCCCCCAGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGACCCCGCCCCCCCGGGACCCCGCCCCCCCCGGGACCCCGCCCCCCGGGATGCCGCCCTCCCCGGGACCCCGCCCCCCGGGACCCCGCCCTCCCCGGGACCCCGCCCCCCGGGACCCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCGCCCCCCCAGGACCCCCGCCCCCCTGTATGCCGCCCT 4 PASS ID=chr18-79617315-INS-274;SVTYPE=INS;SVLEN=274;TIG_REGION=h1tg026073l:72305-72578;QUERY_STRAND=+;HOM_REF=0,16;HOM_TIG=0,16;SVANN=TANDEM;AC=2;NumCollapsed=1;NumConsolidated=1;CollapseId=629.0 GT:AD:DP:SAC:DR:DV:GQ:SUPP 0/1:.,.:.:.:4:3:18:7 chr18 79617369 chr18-79617370-INS-97 G GACCCCGCCCTCCCCGGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCGCCCCCCCAGGACCCCCGCCCCCCTGT 4 . ID=chr18-79617370-INS-97;SVTYPE=INS;SVLEN=97;TIG_REGION=h2tg024158l:18518-18614;QUERY_STRAND=+;HOM_REF=0,1;HOM_TIG=0,1;AC=1;NumCollapsed=2;NumConsolidated=2;CollapseId=629.1 GT:AD:DP:DR:DV:GQ:SAC:SUPP 0/1:3,4:7:3:4:18:2,1,2,2:7 -chr18 79618581 pbsv.DEL.1444 TTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCCGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACAC T 2 PASS SVTYPE=DEL;SVLEN=-832;SVANN=TANDEM;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=630.6 GT:AD:DP:SAC:SUPP 0/1:8,1:9:4,4,0,1:4 +chr18 79618581 pbsv.DEL.1444 TTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCCGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACAC T 2 PASS SVTYPE=DEL;SVLEN=-832;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:8,1:9:4,4,0,1:4 chr18 79618582 Sniffles2.DEL.3BBS11 TGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACT T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-176;SUPPORT=2;COVERAGE=7,6,6,9,9;STRAND=+-;AF=0.286;STDEV_LEN=0;STDEV_POS=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:6:5:2:2 chr18 79618663 Sniffles2.INS.1FFS11 C CACTGTTTACACGCTAACAGGATGACAGACACTGTGTGAAATCAGTCAGTGTGAGCC 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=60;SUPPORT=3;COVERAGE=7,6,6,8,9;STRAND=-;AF=0.5;STDEV_LEN=1.732;STDEV_POS=87.757;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:21:3:3:2 chr18 79618897 pbsv.DEL.1445 CGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCCGTGTGAGCACACTGTTTACACGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGT C 2 PASS SVTYPE=DEL;SVLEN=-652;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:8,1:9:4,4,0,1:4 +chr18 79619105 pbsv.DEL.1446 CCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCCCACTGTTTACATGCTAACAGGAT C 2 PASS SVTYPE=DEL;SVLEN=-828;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:8,1:9:4,4,0,1:4 chr18 79619227 pbsv.DEL.1447 ACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAG A 2 PASS SVTYPE=DEL;SVLEN=-531;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:8,1:9:4,4,0,1:4 chr18 79619246 chr18-79619247-INS-64 A ATCAGTCAGTGCGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAG 4 . ID=chr18-79619247-INS-64;SVTYPE=INS;SVLEN=64;TIG_REGION=h1tg026073l:74513-74576;QUERY_STRAND=+;HOM_REF=0,5;HOM_TIG=0,5;AC=1 GT:SUPP 1/0:1 chr18 79619330 Sniffles2.INS.200S11 T CGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACG 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=61;SUPPORT=5;COVERAGE=9,9,9,9,8;STRAND=+-;AF=0.556;STDEV_LEN=2.51;STDEV_POS=87.918;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:26:4:5:2 @@ -1970,8 +1977,9 @@ chr18 79764427 Sniffles2.DEL.3C6S11 TAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGT chr18 79764429 pbsv.DEL.1478 GTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCACGGTCACCAGCAGTGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTATGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAG G 2 PASS SVTYPE=DEL;SVLEN=-688;SVANN=TANDEM;AC=2 GT:AD:DP:SAC:SUPP 1/1:1,9:10:1,0,5,4:4 chr18 79764518 Sniffles2.DEL.3CAS11 CCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCACGGTCACCAGCAGTGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTATGAGTGACCAGGGTCACCAGCAGCGTAGTC C 0 PASS IMPRECISE;SVTYPE=DEL;SVLEN=-558;SUPPORT=9;COVERAGE=9,9,9,10,10;STRAND=+-;AF=1;STDEV_LEN=0.548;STDEV_POS=100.241;AC=2 GT:GQ:DR:DV:SUPP 1/1:25:0:9:2 chr18 79764530 chr18-79764531-DEL-516 GTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAACCCCATGTGTGAGTGACCACGGTCACCAGCAGTGTAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTA G 4 . ID=chr18-79764531-DEL-516;SVTYPE=DEL;SVLEN=-516;TIG_REGION=h2tg008684l:117208-117208;QUERY_STRAND=+;HOM_REF=0,24;HOM_TIG=0,24;AC=1 GT:SUPP 0/1:1 -chr18 79765161 chr18-79765162-DEL-86 CCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGT C 4 . ID=chr18-79765162-DEL-86;SVTYPE=DEL;SVLEN=-86;TIG_REGION=h2tg008684l:117323-117323;QUERY_STRAND=+;HOM_REF=0,124;HOM_TIG=0,38;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=641.1 GT:SUPP 0/1:1 +chr18 79765161 chr18-79765162-DEL-86 CCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGT C 4 . ID=chr18-79765162-DEL-86;SVTYPE=DEL;SVLEN=-86;TIG_REGION=h2tg008684l:117323-117323;QUERY_STRAND=+;HOM_REF=0,124;HOM_TIG=0,38;AC=1 GT:SUPP 0/1:1 chr18 79765254 Sniffles2.DEL.3C8S11 CCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGTCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTAGCCCCAA C 0 PASS IMPRECISE;SVTYPE=DEL;SVLEN=-127;SUPPORT=4;COVERAGE=9,10,10,10,10;STRAND=+;AF=0.4;STDEV_LEN=0;STDEV_POS=147.785;AC=1 GT:GQ:DR:DV:SUPP 0/1:23:6:4:2 +chr18 79765504 chr18-79765505-DEL-85 GCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTA G 4 . ID=chr18-79765505-DEL-85;SVTYPE=DEL;SVLEN=-85;TIG_REGION=h2tg008684l:117580-117580;QUERY_STRAND=+;HOM_REF=0,3;HOM_TIG=0,3;AC=1 GT:SUPP 0/1:1 chr18 79771040 Sniffles2.INS.215S11 C TCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCTCCACACCGTCCTCCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCATGCCA 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=204;SUPPORT=3;COVERAGE=5,5,5,5,4;STRAND=+-;AF=0.6;STDEV_LEN=19.399;STDEV_POS=23.587;SUPPORT_LONG=0;AC=1 GT:GQ:DR:DV:SUPP 0/1:11:2:3:2 chr18 79771055 pbsv.INS.1479 C CGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCATGCCAGCCTCCCCTCCACACCGTCCTCCCCTCCACGCCATCCTCCCCTCCACGCCATCCTCCCCTCCACGCCGTCCTCCCCTCCACAGCGGCCTCCCCTCCACAGCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGGCCTCCCCTCCACGGCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGGCCTCCCCCTCCACGGCGGCCTCCCCTCCACGCCGTCCTCCCCTCCAC 2 PASS SVTYPE=INS;SVLEN=375;SVANN=TANDEM;AC=1 GT:AD:DP:SAC:SUPP 0/1:4,1:5:2,2,1,0:4 chr18 79771177 chr18-79771178-INS-715 C CCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCATGCCAGCCTCCCCTCCACACCGTCCTCCCCTCCATGCCAGCCTCCCCTCCACACCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACGCCATCCTCCCCTCCACACCGTCCTCCCCTCCACGCCAGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCATGCCAGCCTCCCCTCCATGACATCCTCCCTTCCATGACATCCTCCCCTCCACGGCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCATCCTCCCCTCCACACAGGGCTCCCCTCCATGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACGCCAGCCTCCCCTCCATGACATCCTCCCCTCCATGACATCCTCCCTTCCACGCCGTCCTCCCCTCCACACCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCATCCTCCCCTCCACAGCGGCCTCCCCTCCACACTGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCAGCCTCCCCTCCATGACATCCTCCCCTCCATGGA 4 . ID=chr18-79771178-INS-715;SVTYPE=INS;SVLEN=715;TIG_REGION=h2tg008684l:123185-123899;QUERY_STRAND=+;HOM_REF=0,0;HOM_TIG=0,0;AC=1;NumCollapsed=1;NumConsolidated=1;CollapseId=642.0 GT:AD:DP:SAC:SUPP 0/1:2,3:5:1,1,2,1:5 diff --git a/repo_utils/answer_key/collapse/inputintragt_removed.vcf b/repo_utils/answer_key/collapse/inputintragt_removed.vcf index 1bd85788..a3239f68 100644 --- a/repo_utils/answer_key/collapse/inputintragt_removed.vcf +++ b/repo_utils/answer_key/collapse/inputintragt_removed.vcf @@ -327,7 +327,7 @@ chr18 28799448 pbsv.INS.494 A ATATATATATATATGTGTATATATATATATATGTGTATATATATATGTGT chr18 28799477 Sniffles2.INS.B0S11 T TGTGTATATATATATGTGTATATATATATGTATATATATATGTGTATATATATATG 3 PASS PRECISE;SVTYPE=INS;SVLEN=56;SUPPORT=5;COVERAGE=6,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=5.859;STDEV_POS=17.01;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9652;PctSizeSimilarity=0.9655;PctRecOverlap=0.4915;SizeDiff=2;StartDistance=-29;EndDistance=-29;GTMatch=.;TruScore=80;MatchId=245.0 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. chr18 28837164 Sniffles2.INS.B1S11 G GGGGAGGGGAGGGGGAGGGGAGGGGGAGGGGAGGGAAGGGGAGGGGGAGGGGAGGGGGAGGGGAGG 3 PASS PRECISE;SVTYPE=INS;SVLEN=66;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9924;PctSizeSimilarity=0.9848;PctRecOverlap=0.9701;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=246.0 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. chr18 28883938 pbsv.INS.496 A ATATATCATATATATGATATATATATCATATAATATCATATATATGATATATATCATATATATCATATATATGATAATATATGA 2 PASS SVTYPE=INS;SVLEN=83;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9521;PctSizeSimilarity=0.988;PctRecOverlap=0.7952;SizeDiff=-1;StartDistance=17;EndDistance=17;GTMatch=.;TruScore=91;MatchId=247.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,4:4:0,0,3,1 -chr18 28883961 chr18-28883962-INS-85 T TCATATAATATCATATATATGATATATATCATATATATCATATATATGATATTATATGATATATATATCATATAATATCATATATA 4 . ID=chr18-28883962-INS-85;SVTYPE=INS;SVLEN=85;TIG_REGION=h1tg005703l:95004-95088;QUERY_STRAND=-;HOM_REF=0,0;HOM_TIG=0,0;AC=1;PctSeqSimilarity=0.9763;PctSizeSimilarity=0.9647;PctRecOverlap=0.9176;SizeDiff=-3;StartDistance=-6;EndDistance=-6;GTMatch=.;TruScore=95;MatchId=247.0 GT 1/0 ./. ./. +chr18 28883963 Sniffles2.INS.B2S11 G TCATATAATATCATATATATGATATATATCATATATATCATATATATGATAATATATGATATATATATCATATAATATCATATATAT 3 PASS PRECISE;SVTYPE=INS;SVLEN=87;SUPPORT=4;COVERAGE=4,4,4,4,3;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9884;PctSizeSimilarity=0.977;PctRecOverlap=0.9655;SizeDiff=-2;StartDistance=-2;EndDistance=-2;GTMatch=.;TruScore=97;MatchId=247.1 GT:GQ:DR:DV ./.:.:.:. 1/1:11:0:4 ./.:.:.:. chr18 29595955 Sniffles2.INS.B3S11 T TATATATATAATATATCATATATTATATATATAATATATCATATATTATATATATAATATATTATATATAAATATATAATATATTATATAATATATATATAATATATATTATATAATATATAATATATTATATATATAATATTATATATATAATATATGATATATTATATATATAATATATCATATATTATATATATAATATATAATATAATATA 3 PASS PRECISE;SVTYPE=INS;SVLEN=219;SUPPORT=3;COVERAGE=6,6,6,6,6;STRAND=-;AF=0.5;STDEV_LEN=2.646;STDEV_POS=3.464;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9724;PctSizeSimilarity=1;PctRecOverlap=0.968;SizeDiff=0;StartDistance=-7;EndDistance=-7;GTMatch=.;TruScore=98;MatchId=248.0 GT:GQ:DR:DV ./.:.:.:. 0/1:21:3:3 ./.:.:.:. chr18 29595959 pbsv.INS.500 T TATTATAATATATTCATATATTATATATATAATATATCATATATTATATATATAATATATTATATATAATATATAATATATTATATAAATATATATAATATATATTATATAATATATAATATATTATATATATAATATATATATATATTTATATGATATATTATATATATATATCATATATTATATATATAATATATTATATAATATATTATATA 2 PASS SVTYPE=INS;SVLEN=214;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9678;PctSizeSimilarity=0.9772;PctRecOverlap=0.9406;SizeDiff=5;StartDistance=-11;EndDistance=-11;GTMatch=.;TruScore=96;MatchId=248.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,6:6:0,0,2,4 chr18 29596662 pbsv.INS.502 A ATTATAATATATATAATATATTATATATTATAATATATATAATATATAGTAT 2 PASS SVTYPE=INS;SVLEN=51;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9806;PctSizeSimilarity=0.9808;PctRecOverlap=0.9623;SizeDiff=1;StartDistance=1;EndDistance=1;GTMatch=.;TruScore=97;MatchId=249.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,6:6:0,0,2,4 @@ -590,7 +590,6 @@ chr18 74361934 pbsv.INS.1204 A AATTATATATTTACGTATAATATAATTTATAATTATATATTTACGTATA chr18 74361935 Sniffles2.INS.168S11 A ATTATATATTACGTATAATATAATTTATAATTATATATTTACGTATAATATAATTTATAATTATATACGTATAATATAATTTATATTATATATGTATATAATATAATTTATAATTATATATTTATATATAATATAATTTATATTATATATGTATATAATATAATTTATAATTATATATTTATATATATATAATTATATATT 3 PASS PRECISE;SVTYPE=INS;SVLEN=201;SUPPORT=4;COVERAGE=6,7,7,7,7;STRAND=+-;AF=0.571;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9901;PctSizeSimilarity=0.995;PctRecOverlap=0.9901;SizeDiff=1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=503.1 GT:GQ:DR:DV ./.:.:.:. 0/1:18:3:4 ./.:.:.:. chr18 74425099 Sniffles2.DEL.365S11 TCCCGTCAGGAAGTCAGTCAGTTTCCCGTCAGGAAGTCAGTCAGTTTCCCATCAGGAAGTCAGTCT T 0 PASS IMPRECISE;SVTYPE=DEL;SVLEN=-65;SUPPORT=10;COVERAGE=11,11,11,11,11;STRAND=+-;AF=0.909;STDEV_LEN=9.39;STDEV_POS=37.007;AC=2;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.9848;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=504.0 GT:GQ:DR:DV ./.:.:.:. 1/1:17:1:10 ./.:.:.:. chr18 74485194 Sniffles2.DEL.366S11 TCCATGATGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCAGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-340;SUPPORT=10;COVERAGE=11,10,10,10,12;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.9971;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=505.0 GT:GQ:DR:DV ./.:.:.:. 1/1:27:0:10 ./.:.:.:. -chr18 74503904 chr18-74503905-INS-54.1 A ACACACGCAGCCACACTGCCGCTGGGACAAATGATGGGCGTCAGGCCATACACTG 4 . ID=chr18-74503905-INS-54.1;SVTYPE=INS;SVLEN=54;TIG_REGION=h2tg010301l:10313-10366;QUERY_STRAND=-;HOM_REF=0,33;HOM_TIG=0,33;AC=1;PctSeqSimilarity=0.9909;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=506.0 GT 0/1 ./. ./. chr18 74503905 Sniffles2.INS.169S11 C CACACCGCAGCCACACTGCCGCTGGGACAAATGAGGGGCGTCAGGCCATACACTG 3 PASS PRECISE;SVTYPE=INS;SVLEN=55;SUPPORT=6;COVERAGE=6,6,6,6,6;STRAND=+-;AF=1;STDEV_LEN=0.5;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9818;PctSizeSimilarity=0.9818;PctRecOverlap=0.9818;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=506.0 GT:GQ:DR:DV ./.:.:.:. 1/1:16:0:6 ./.:.:.:. chr18 74617097 Sniffles2.INS.16BS11 A CACACATCCATATCCGTACACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACGCATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCATACACCACACACATCTATATCCACACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCATACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACACACCACACACATCCATATCCATGCTCCACACACATCTATATCCACACACATCCATATCCACACACATCCATATCCACACACCACATACATCCATATCCACGCACATCCATATCCACATGCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATTCATATCCATACACCACACACACCCATATCCACACACCATACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCGATATCCACGTACATCCATATCCACGCACCACACACATCCATATCCATGCACATCCATATCCACACACATCCATATCCACTCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATGTCCACACACATCCATATCCACACACCACACACATCCATATTCACACACATCCATATCCGCACACCACACACATCCATATTCACACACATCCATATCCACGCACATCCATATCTATGCACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCGACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACC 3 PASS PRECISE;SVTYPE=INS;SVLEN=1997;SUPPORT=4;COVERAGE=6,4,4,4,6;STRAND=+-;AF=1;STDEV_LEN=1.414;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9997;PctSizeSimilarity=1;PctRecOverlap=0.9995;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=507.0 GT:GQ:DR:DV ./.:.:.:. 1/1:11:0:4 ./.:.:.:. chr18 74617136 pbsv.INS.1211 A ACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACGCATCCATATCCACACACCACACATATCCATATCCACACAGCACACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCATACACCACACACATCTATATCCACACACCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACATCCATATCCACACACCACACACACCCATATCCACACACCACACACACCCATATCCACACACCACACACATCCATATCCACACATCCATATCCATGCACCACACACATCCATATCCACACACATCCATTTCCACGCACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCATACACATCCATATCCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCCACACACCACACACATCCATATCCATGCTCCACACACATCTATATCCACACACATCCATATCCACACACATCCATATCCACACACCACATACATCCATATCCACGCACATCCATATCCACATGCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATTCATATCCATACACCACACACACCCATATCCACACACCATACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCGATATCCACGTACATCCATATCCACGCACCACACACATCCATATCCATGCACATCCATATCCACACACATCCATATCCACTCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATGTCCACACACATCCATATCCACACACCACACACATCCATATTCACACACATCCATATCCGCACACCACACACATCCATATTCACACACATCCATATCCACGCACATCCATATCTATGCACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCATGCACCACACACATCCATATCCACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACACACATCCATATCCACGCACCACACACATCCATATCGACACACCACACACATCCATATCCACACACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACACATCCATATCCACGCACCACACATCCATATCCACGCACCACACACATCCATATCCATG 2 PASS SVTYPE=INS;SVLEN=1996;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9982;PctSizeSimilarity=0.9995;PctRecOverlap=0.98;SizeDiff=1;StartDistance=-40;EndDistance=-40;GTMatch=.;TruScore=99;MatchId=507.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:2,4:6:1,1,1,3 @@ -626,7 +625,6 @@ chr18 76967654 Sniffles2.INS.17FS11 T TGAGATTTGTGATTTGGTGTTGGAGGTGGTGGTGTGCTCTGT chr18 76975155 Sniffles2.INS.180S11 C CTTTTCTTTTCTTTTCTTCTTTTCTTTTCTTTTCTTTTCTTTCTTTCTTTTCTTTTCTTTT 3 PASS PRECISE;SVTYPE=INS;SVLEN=61;SUPPORT=7;COVERAGE=7,7,7,7,7;STRAND=+-;AF=1;STDEV_LEN=6.504;STDEV_POS=11.628;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.976;PctSizeSimilarity=0.9683;PctRecOverlap=0.9683;SizeDiff=2;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=97;MatchId=532.0 GT:GQ:DR:DV ./.:.:.:. 1/1:19:0:7 ./.:.:.:. chr18 76975158 pbsv.INS.1267 T TTCTTTTCTTTTCTTTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 2 PASS SVTYPE=INS;SVLEN=62;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9843;PctSizeSimilarity=0.9841;PctRecOverlap=0.9365;SizeDiff=1;StartDistance=-4;EndDistance=-4;GTMatch=.;TruScore=96;MatchId=532.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,7:7:0,0,3,4 chr18 77044932 Sniffles2.INS.181S11 A CCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGCCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGACCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3 PASS PRECISE;SVTYPE=INS;SVLEN=326;SUPPORT=6;COVERAGE=11,11,11,11,11;STRAND=+-;AF=0.545;STDEV_LEN=1.414;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9969;PctSizeSimilarity=0.9969;PctRecOverlap=0.9939;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=533.0 GT:GQ:DR:DV ./.:.:.:. 0/1:33:5:6 ./.:.:.:. -chr18 77045365 chr18-77045366-INS-87.1;pbsv.INS.1274 T TTGACCCGCTGCAGCAGCACCTGGCTGCACCAGGTCAGGGTCTCTGGAGCCTGGCTGCCAGCAGAGACATTTGCATGCGTCTCTGGAC 4 PASS ID=chr18-77045366-INS-87.1;SVTYPE=INS;SVLEN=87;TIG_REGION=h2tg018293l:94840-94926;QUERY_STRAND=-;HOM_REF=0,22;HOM_TIG=0,22;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9943;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=533.1 GT:AD:DP:SAC 0/1:.:.:. ./.:.:.:. 0/1:6,5:11:2,4,2,3 chr18 77045366 Sniffles2.INS.182S11 T TGACCCGCTGCAGCAGCACCTGGCTGCACCAGGTCAGGGTCTCTGGAGCCCGGCTGCCAGCAGAGACATTTGCATGCGTCTCTGGAC 3 PASS PRECISE;SVTYPE=INS;SVLEN=87;SUPPORT=11;COVERAGE=11,11,11,11,11;STRAND=+-;AF=1;STDEV_LEN=0.378;STDEV_POS=1.134;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9943;PctSizeSimilarity=1;PctRecOverlap=0.9885;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=533.1 GT:GQ:DR:DV ./.:.:.:. 1/1:30:0:11 ./.:.:.:. chr18 77057815 Sniffles2.DEL.37BS11 GCGGGGAGTGTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTTTTTTTAATAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTGTCGATCTCCTGACCTCGTGTTCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG G 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-301;SUPPORT=8;COVERAGE=9,8,8,8,6;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.9967;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=534.0 GT:GQ:DR:DV ./.:.:.:. 1/1:22:0:8 ./.:.:.:. chr18 77082733 Sniffles2.INS.183S11 G GAGGAATCCTTCCTCCCTGCAGCAGCTGGCTGTCATAGGTGGTCTAGGGAACGCCATGTGGCTCAGAAGGACGAGGAATCCTTCCTCCCTGCTGCAGCTAGCTGTCATAGGTGGTCTAGGGAACGCCATGTGGCTCAGAAGGAC 3 PASS PRECISE;SVTYPE=INS;SVLEN=144;SUPPORT=3;COVERAGE=6,5,5,5,5;STRAND=+-;AF=0.6;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9965;PctSizeSimilarity=1;PctRecOverlap=0.9931;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=535.0 GT:GQ:DR:DV ./.:.:.:. 0/1:11:2:3 ./.:.:.:. @@ -641,10 +639,9 @@ chr18 77373158 Sniffles2.DEL.37ES11 CCCACGCTCAGGACCCCTCTCCCCACCTCACACCTCAGCCACGC chr18 77373380 Sniffles2.DEL.37FS11 CCACCTCACACCCCAGCCAAGCCCAGGACCCACACTCACGGTTCCGCTCCCCACCTCAAACCCCGACCAAGCCCAGGACCCACGCTCACGGCCCTACTCCCCACCTCACACCCCGACCAAGTCCAGGACCCATGCTCACGGTTCCGCTCCCCACCTCACACCCCGAGCAAGTCCAGGACCCATGCTCATGGCCCCGCTCTC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-200;SUPPORT=6;COVERAGE=9,9,9,9,9;STRAND=+-;AF=0.667;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.995;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=542.1 GT:GQ:DR:DV ./.:.:.:. 0/1:13:3:6 ./.:.:.:. chr18 77549559 pbsv.INS.1297 C CTTCCTGGCTGTGACCAGACAACCCTAGTCTCTGCCTGTGTCTCACTCGGTG 2 PASS SVTYPE=INS;SVLEN=51;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9903;PctSizeSimilarity=1;PctRecOverlap=0.9804;SizeDiff=0;StartDistance=1;EndDistance=1;GTMatch=.;TruScore=99;MatchId=543.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,4:4:0,0,1,3 chr18 77555042 Sniffles2.DEL.380S11 TTTATATCCTTAGTCATTCATGGTGAAACAAATCATTGGGGAGAAAAATGAACAAAAAAACCCCAGAAGTTTTGTAAGTTCTAATATGCATAGGCTCTGGCTCTATTCTCTGGTGAGAAGGTTTCTGCTAGGCCCACAGTTTATAATATAAATACATATTTCTCTACACTCATGTAATCCAGAGGACCTGTAGATGAACTCCAGAGCTGTAATCAAGGTCAAATGACATCACGTGAAGACCCAGTGCTCAAAATATAACCACTAGTAATACACTGGAGCACATACTTGGAGATGTTTTGCTGATAGTTATAGGTAAAACTAAATTGTGTGTGTGTGTGTGTGTGTGTGTGCACATATATGTCTACATAAGTATACAGTCAGACTTTCATATCCTTGGGATTCACATCTGTGAATTCAAGCAACCTTGGATAAAAACTATTCGAAAAAAAATTGCATCTGTACTGAACATGTACAGGCTTTTTTACCTTGTCATTATTCCATAAACGATACAGTATAACAACTATTTATACATTTACATTTAATTAGATATCATAAGCAATCTAGAAATGATTCAAAGAGGTGGAATGGTGTGCATAGCTTATATGCAAATATTACACCATTTTATATCAGATACTTGAGCATCCATGGATTTTGGTACCATTGGGAGGTCCTGGAACCAATCCCACATGGACACCAAGGGATGACTGTATAATCTATGAGTATAACTGTATTTTTATCTATGTTATTATGTTGATAGCTACATAAAATTGCATTGTGTAGATGTATAATAATTTTTAACATTTATTTATTGAATATTTATTTCCACCAAGACACAGTAAACAACTTTGTGCATACATCTTTACATATTTAAACATCATTTCTAAAAAAATTAATTCACCAAAATTGGATTTTAGATGATAGATAGATAGATAGATACAGAGAGATAGATAGACAGATAGAGGATATGGTCTATATGGTTCATTAATGGCCCAATGATTAAAATCACTCATGATCCAAAGATTATGAGATCCAAATATATATATATGTAAAGTTGAACATAGTTTGATTTATATCATCATGATTTTTAGCAGCAAAGGTATAATTCTATACCTAAAGTACTAAGCTTTTATGAAGATTTTGTTTCTGTTTACTCTGAATTATCT T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-1162;SUPPORT=3;COVERAGE=4,3,3,3,4;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=0.9996;PctSizeSimilarity=1;PctRecOverlap=0.9991;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=544.0 GT:GQ:DR:DV ./.:.:.:. 1/1:8:0:3 ./.:.:.:. -chr18 77957441 chr18-77957442-INS-96 A ACTCCAACACCACCACCACGAGCACCCCAAAAACACTATCACCCCAACAACTCCAACACCACCACCAACACCAGCACCACCAATAACACTATCACCC 4 . ID=chr18-77957442-INS-96;SVTYPE=INS;SVLEN=96;TIG_REGION=h2tg001461l:175280-175375;QUERY_STRAND=-;HOM_REF=0,1;HOM_TIG=0,1;AC=1;PctSeqSimilarity=0.9697;PctSizeSimilarity=0.96;PctRecOverlap=0.9604;SizeDiff=4;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=96;MatchId=547.0 GT 0/1 ./. ./. chr18 77957442 Sniffles2.INS.18CS11 C CAACTCCAACACCACCACCACCAGCACCACCAATAACACTATCACCCCAACAACTCCAACACCACCACCAACACCAGCACCACCAATAACACTATCACCC 3 PASS PRECISE;SVTYPE=INS;SVLEN=100;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=2.309;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.995;PctSizeSimilarity=1;PctRecOverlap=0.9901;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=547.0 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. -chr18 77957622 Sniffles2.INS.18DS11 C CCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCCAAAAACACTACCACCCCAACAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACCGCCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCA 3 PASS PRECISE;SVTYPE=INS;SVLEN=255;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9961;PctSizeSimilarity=0.9961;PctRecOverlap=0.9922;SizeDiff=1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=547.1 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. -chr18 77958111 Sniffles2.INS.18ES11 C CAACAACTCCAACCCCACTGCCAACACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACAACCACCACGAGCACCCCCAATAACACTATCACCC 3 PASS PRECISE;SVTYPE=INS;SVLEN=103;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9952;PctSizeSimilarity=1;PctRecOverlap=0.9903;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=547.2 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. +chr18 77957622 Sniffles2.INS.18DS11 C CCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCACCCCCAAAAACACTACCACCCCAACAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACTCCAACACCACCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACCGCCACCACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACCACTGCCAACACCAGCA 3 PASS PRECISE;SVTYPE=INS;SVLEN=255;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9961;PctSizeSimilarity=0.9961;PctRecOverlap=0.9922;SizeDiff=1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=547.2 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. +chr18 77958111 Sniffles2.INS.18ES11 C CAACAACTCCAACCCCACTGCCAACACCAGCACCCCCAATAACACTATCACCCCAACAACTCCAACACAACCACCACGAGCACCCCCAATAACACTATCACCC 3 PASS PRECISE;SVTYPE=INS;SVLEN=103;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9952;PctSizeSimilarity=1;PctRecOverlap=0.9903;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=547.3 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. chr18 78010175 Sniffles2.INS.18FS11 G GTGGTGGTGATAGTGATGATGATGGTGGTGATGGTGTTGCTAGTGGTAATGGCAGTGATAATGATGCTGGTGGTGGTGATGGTGGTGATGGTAGTGATGATGATGGTGGTGATGGTGTTAGTGTTGGTAGTGGGAATGGTAGTGATGGTGGTGGTGGGTGGCGATGGTGCTGGTGGTGATGAGAATGGTTGTGTTGGTGGTGGCAGTAGTGATGGTGATGACTGTAGTGGTGATGGTGGTGGTGATAGTGATGGTGGTGGTGGTGGTGGTGATGGTGGTGATGATGGTGATGGTGATAGTGGTGGTGATAGTGGTGGTAGTGACAGTGGTAGTGATGGTGGCAGTAGTGATGGTGATGATGGTGTTGGTGATGGTGGTGGTGATGGTGGTGATGATGGTGATGGTGATAGTGGTGGTGATGGTGGTGGTAGTGACAGTGGTAGTGATGGTGGCAGTAGTGATGGTGATGATGGTGTTGGTGATGGTGGTGGTGGTGGTGATGATGGTGATGGTGATGATGATGGTGGTGGTGGTGAGGATGGTGATAGTGAGGATGATGGTGGTGGTGGTGATGGTGGTGGTGATAGTGATGATGGTGTTGGTGATGGTGATGGTGATGATGTTGATTGTGATGGTGGTGGTGGTGATAGTGATATGGTGATGGTGGTGGTGAAGGTGATGGTGATGGTGGTGGTGGTGGTGGTGAGGATGGTGATAGTGAGGATGATGGTGGTGGTGGTGGTGATGGTGGTGGTGGAGGTGGTGATAGTGATGATGGTGTTGGTGATGGTGATGGTGATGATGGTGATGATGTTGACTGTGATGGTGGTGGTGGTGATGGTGATATGGTGATGGTGGTGGTGATGGTGATGATGGTGATGGTGATGATGTTGACTGTGATGGTG 3 PASS PRECISE;SVTYPE=INS;SVLEN=905;SUPPORT=9;COVERAGE=9,9,9,9,11;STRAND=+-;AF=1;STDEV_LEN=0.837;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9989;PctSizeSimilarity=0.9989;PctRecOverlap=0.9989;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=548.0 GT:GQ:DR:DV ./.:.:.:. 1/1:25:0:9 ./.:.:.:. chr18 78041170 pbsv.DEL.1314 TTACAATTTACTTGGTTTGGGGGCTTAGATTCACAGATGGTTTCTTTCGCTT T 2 PASS SVTYPE=DEL;SVLEN=-51;AC=1;PctSeqSimilarity=0.9905;PctSizeSimilarity=0.9808;PctRecOverlap=0.9811;SizeDiff=1;StartDistance=-1;EndDistance=0;GTMatch=.;TruScore=98;MatchId=549.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:5,4:9:4,1,3,1 chr18 78041171 Sniffles2.DEL.389S11 TACAATTTACTTGGTTTGGGGGCTTAGATTCACAGATGGTTTCTTTCGCTTTAA T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-53;SUPPORT=4;COVERAGE=9,9,9,9,9;STRAND=+-;AF=0.444;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=0.9813;PctSizeSimilarity=0.9811;PctRecOverlap=0.9444;SizeDiff=-1;StartDistance=-2;EndDistance=-3;GTMatch=.;TruScore=96;MatchId=549.0 GT:GQ:DR:DV ./.:.:.:. 0/1:26:5:4 ./.:.:.:. @@ -670,11 +667,9 @@ chr18 78502801 Sniffles2.INS.1A8S11 G GCTGTACCGGGACAGGGCATGGCCCGTCTCGATCCCTTAGCG chr18 78502801 Sniffles2.INS.1A7S11 G GCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCCGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCCGCTGTACCGGGACAGGGCCATGGCCGTCTCGATCCTTAGCGCTGGCCCGCTGTACCGGGACAGGGCATGGCCGCCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCTGCTGTACCGGGACAGGGCATGGCCGTCTCGATCCTTAGCGCTGGCCT 3 PASS PRECISE;SVTYPE=INS;SVLEN=658;SUPPORT=3;COVERAGE=7,9,9,9,9;STRAND=+-;AF=0.333;STDEV_LEN=1;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9977;PctSizeSimilarity=1;PctRecOverlap=0.9985;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=570.1 GT:GQ:DR:DV ./.:.:.:. 0/1:13:6:3 ./.:.:.:. chr18 78504366 Sniffles2.DEL.396S11 CCTGAGGATGCCAGCCCGACAGAGCACGGTGTCGGCCAGGAGGAGGATGGAC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-51;SUPPORT=5;COVERAGE=10,10,10,10,10;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.9808;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=571.0 GT:GQ:DR:DV ./.:.:.:. 0/1:36:5:5 ./.:.:.:. chr18 78513048 Sniffles2.INS.1A9S11 C CTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGAT 3 PASS PRECISE;SVTYPE=INS;SVLEN=51;SUPPORT=5;COVERAGE=5,5,6,7,7;STRAND=+-;AF=0.833;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9903;PctSizeSimilarity=1;PctRecOverlap=0.9804;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=572.0 GT:GQ:DR:DV ./.:.:.:. 1/1:3:1:5 ./.:.:.:. -chr18 78513495 pbsv.SPLIT.DUP.1354 G GCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAACCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCC 0 PASS SVTYPE=INS;SVLEN=1418;AC=1;PctSeqSimilarity=0.9796;PctSizeSimilarity=0.9601;PctRecOverlap=0.9397;SizeDiff=59;StartDistance=-60;EndDistance=-60;GTMatch=.;TruScore=95;MatchId=572.9 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:7,2:9:0,7,1,1 chr18 78513645 Sniffles2.INS.1ABS11 T TCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAG 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=102;SUPPORT=2;COVERAGE=7,7,7,8,9;STRAND=+-;AF=0.286;STDEV_LEN=21.92;STDEV_POS=98.288;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9854;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=398;EndDistance=398;GTMatch=.;TruScore=66;MatchId=572.2 GT:GQ:DR:DV ./.:.:.:. 0/1:6:5:2 ./.:.:.:. chr18 78514220 pbsv.INS.1355 C CCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTT 2 PASS SVTYPE=INS;SVLEN=2039;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9998;PctSizeSimilarity=0.9995;PctRecOverlap=0.999;SizeDiff=1;StartDistance=0;EndDistance=0;GTMatch=.;TruScore=99;MatchId=572.3 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:4,2:6:2,2,0,2 chr18 78514296 pbsv.INS.1356 C CCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAAGAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGATCTACTAACAGTGGGTCAGCAGACACTACCCCAAGTATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTACCGCAAGAGTCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGCACTACCCCAAGAATCAGCCTATCTAGACCTACTAACAGTGGGTCAGCAGACACTGCCCCAAGAATCAGCCTATTTAGACCTACTAACAGTGGGTCAGCAGACACTACCCAGGGGCCCAAGGAAAGACATACTCAGCCTACCACTG 2 PASS IMPRECISE;SVTYPE=INS;SVLEN=2024;AC=1;PctSeqSimilarity=0.9616;PctSizeSimilarity=0.9922;PctRecOverlap=0.9588;SizeDiff=16;StartDistance=-76;EndDistance=-76;GTMatch=.;TruScore=97;MatchId=572.3 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:8,1:9:1,7,1,0 -chr18 78514605 Sniffles2.INS.1AFS11 C CCCCAAGCATCAGCCTATCTAGTTCTACTAACAGTGGGTCAGCAGACACTG 3 PASS PRECISE;SVTYPE=INS;SVLEN=51;SUPPORT=2;COVERAGE=9,8,4,4,4;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9515;PctSizeSimilarity=0.9808;PctRecOverlap=0;SizeDiff=1;StartDistance=-491;EndDistance=-491;GTMatch=.;TruScore=64;MatchId=572.6 GT:GQ:DR:DV ./.:.:.:. 0/1:14:2:2 ./.:.:.:. chr18 78517827 pbsv.INS.1358 G GTCAGGCACAGAGCCCGGCGCCCTGTCTCGGAAGCGGGGCCCTCAGGCACAGAGCCCGCCGCCTTGTCCCGGAAGCGGGGCCGTCAGGCACAGAGCCCGGCGCCTTGTCTCGGAAGCGGGGCCCTCAGGCACAGAGCCCGCCGCCTTGTCCGGAAGCGGGGCCGTCAGGCACAGAGCCCGGCGCCCTGTCTCGGAAGCGGGGCCCTCAGGCACAGAGCCCGCCGCCTTGTCCCGGAAGCGGGGCCCTCAGGCACAGAGCCCGGCGCCTTGTCCCGGAAGCAAGGCCT 2 PASS SVTYPE=INS;SVLEN=286;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9965;PctSizeSimilarity=0.9931;PctRecOverlap=0.9931;SizeDiff=2;StartDistance=1;EndDistance=1;GTMatch=.;TruScore=99;MatchId=574.1 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:3,2:5:0,3,0,2 chr18 78548659 pbsv.INS.1360 A AACTGCACACACACTCTGTACACACGCACACACCCACGCAACACTGTACAC 2 PASS SVTYPE=INS;SVLEN=50;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9901;PctSizeSimilarity=0.9804;PctRecOverlap=0.9804;SizeDiff=1;StartDistance=1;EndDistance=1;GTMatch=.;TruScore=98;MatchId=577.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:3,1:4:1,2,0,1 chr18 78563775 Sniffles2.INS.1BAS11 C CCCACACTCTGCACCCCTCAAACCCCCACACCTCTCAAACCCCCACACCCCCACCCCCCCACATCCCACACCCCACACTCCTCAAACCTCCACACCCCACACCCCCACATCCCACACCCCACACTCCTCAAACCTCCACACCCCACACCCCACACTCTGCACCCCTCAAACCCCCACACCTCTCAAAC 3 PASS PRECISE;SVTYPE=INS;SVLEN=188;SUPPORT=2;COVERAGE=4,4,4,4,4;STRAND=+;AF=0.5;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9571;PctSizeSimilarity=0.9787;PctRecOverlap=0.7302;SizeDiff=-4;StartDistance=49;EndDistance=49;GTMatch=.;TruScore=88;MatchId=578.0 GT:GQ:DR:DV ./.:.:.:. 0/1:14:2:2 ./.:.:.:. @@ -698,7 +693,7 @@ chr18 78866564 pbsv.DEL.1389 TGCAGTGCTGGCTAGAGGGAGGGTGACAGCCGCGGACAAACCTGCAGACCT chr18 78965175 Sniffles2.INS.1C8S11 T TCGGTGGCACCCAGGCTGCCCCTCCACCCGGCCTGCACCAGCGCCGCCTTCTCCGGAGCCGTCGGTGGGACCCAGGCTGCCCCTCCACCCGGCCTGCGCCAGCGCCGCCTTCTCTGGGAGCCA 3 PASS PRECISE;SVTYPE=INS;SVLEN=124;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.996;PctSizeSimilarity=0.9919;PctRecOverlap=0.984;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=596.0 GT:GQ:DR:DV ./.:.:.:. 1/1:13:0:5 ./.:.:.:. chr18 78965181 pbsv.INS.1392 G GCACCCAGGCTGCCCCTCCACCCGGCCTGCACCAGCGCCGCCTTCTCCGGAGCCGTCGGTGGGACCCAGGCTGCCCCTCCACCCGGCCTGCGCCAGCGCCGCCTTCTCTGGGAGCCATCGGTGG 2 PASS SVTYPE=INS;SVLEN=123;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9919;PctSizeSimilarity=1;PctRecOverlap=0.9431;SizeDiff=0;StartDistance=-7;EndDistance=-7;GTMatch=.;TruScore=97;MatchId=596.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,5:5:0,0,4,1 chr18 79033948 Sniffles2.INS.1D3S11 A ACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATATCTCAGAGCCTTCCACAGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCAC 3 GT PRECISE;SVTYPE=INS;SVLEN=148;SUPPORT=2;COVERAGE=8,8,8,8,8;STRAND=-;AF=0.25;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9798;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-298;EndDistance=-298;GTMatch=.;TruScore=65;MatchId=600.1 GT:GQ:DR:DV ./.:.:.:. 0/1:3:6:2 ./.:.:.:. -chr18 79034317 chr18-79034318-INS-74 A AACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCATG 4 . ID=chr18-79034318-INS-74;SVTYPE=INS;SVLEN=74;TIG_REGION=h2tg020617l:81367-81440;QUERY_STRAND=+;HOM_REF=0,62;HOM_TIG=0,72;AC=1;PctSeqSimilarity=0.9667;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-223;EndDistance=-223;GTMatch=.;TruScore=65;MatchId=600.2 GT 0/1 ./. ./. +chr18 79034325 Sniffles2.INS.1D2S11 C CCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCAC 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=74;SUPPORT=3;COVERAGE=8,8,8,8,8;STRAND=+-;AF=0.375;STDEV_LEN=1;STDEV_POS=65.241;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.98;PctSizeSimilarity=1;PctRecOverlap=0.8933;SizeDiff=0;StartDistance=-8;EndDistance=-8;GTMatch=.;TruScore=95;MatchId=600.3 GT:GQ:DR:DV ./.:.:.:. 0/1:16:5:3 ./.:.:.:. chr18 79035861 Sniffles2.INS.1D8S11 A AGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATATCTCAGAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCAG 3 PASS PRECISE;SVTYPE=INS;SVLEN=296;SUPPORT=3;COVERAGE=8,7,7,7,7;STRAND=-;AF=0.429;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9916;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=454;EndDistance=454;GTMatch=.;TruScore=66;MatchId=601.1 GT:GQ:DR:DV ./.:.:.:. 0/1:18:4:3 ./.:.:.:. chr18 79036240 pbsv.INS.1399 C CGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCAAGGCTGCCATATCTCAGAGCCTTCCACGACTCTCACCCTCCACCCAGGCATCCTGGTTCTAGATTCAGTCCTCATGGCTGCCATGTCTCATAGCCTTCCAT 2 PASS SVTYPE=INS;SVLEN=148;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9664;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-380;EndDistance=-380;GTMatch=.;TruScore=65;MatchId=601.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:7,2:9:2,5,0,2 chr18 79039224 pbsv.INS.1400 G GATGGTATGGTATGCTAAGGTTCTCATGGATGGTACTCTACGCTAAGGTTCTCGTGGATGGTACTCTATGCTAAGGTTCTCGTGGATGGTACTCTATGCTAAGGTTCTCGTGGATGGTACTCTATGCTAAGGTTCTCTGGATGGTACTCTATGCTAAGGTTCTCATGGATGGTACTCTATGCTAAGGTTCTCAGATGGTACTTTATGCTAAGGTTCTCAGATGGTATTTTATGCTAAGGTTCTCAGATGGTATTTTATGCTAAGGTTCTCAGATGGTACTTTATGCTAAGGTTCTCATGGATGGTACTTTATGCTAAGGTTCTCATGGATGGTACTCTATGCTAAGGTTCTTGTGGATGGTACAGTATGCTAAGGTTCTCGTGGATGGTACTCTATGCTGAGGTTCTCATGGATGGTACTTTCTCGTGGATAGTACTATACTGCTAAGGTTCTTGCGGTTGGTACTCTATGCTAAGGTTCTCACGGATGGTACTCTGTGCTAAGGTTCTCACGGATGGTACTCTGTGCTAAGGTTCTCGTGGATGGTACTCTGTGCTAAGGTTCTCGGATGGTACTCTGTGCTAAGGTTCTTGTGGATGTACTCTATGCTAAGGTTCTCGTGGATGGTACTTTCTCATGAATAGTACTGTACTACTAAGGTTCTCATGGATGGTACTCTATGCTAAGGTTCTTGTGGATGGTACTCTATGCTAAGGTTCTCGTGGATGGTACTTTCTCATGAATAGTACTGTACTACTAAGGTTCTCATGGATGGTACTCTATGCTAAGGTTCTTGTGGATGGTACTTTCTCATGGATAGTACTATACTGCTAAGGTTCTCGTGGCTGGTACTGCATGCTAAGGTTCTCGTGGATGGTACTTTCTCGTGGATAGTACTATACTGCTAAGGTTCTCGTGGATGGTACTCTATGCTAAGGTTCTCAAATGGTACTCTATGCTAAGGTTCTCAGATGGTACTTTATGCTAAGGTTCTCAGATGGTACTTTATGCTAAGGTTCTCATGGATGGTACTTTATGCTAAGGTTCTCATGGATGGTACTCTATGCTAAGGTTCTTGTGGATGGTACAGTATGCTAAGGTTCTCGTGGATGGTACTCTATGCTAAGGTTCTCATGGATGGTACTTTCTCATGGATAGTACTATACTGCTAATGTTCTTGCGGTTGGTACTCTATGCTAAGGTTCTCACGGATGGTACTCTGTGCTAAGGTTCTCGCGGATGGTACTCTGTGCTAAGGTTCTCGCGGATGGTACCGTATGCTAAGGGTCTCGCGGATGGTACTCTATGCTAAGGTTCTCGTGGATGGTACTTTCTCATGA 2 PASS SVTYPE=INS;SVLEN=1339;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9955;PctSizeSimilarity=0.997;PctRecOverlap=0.9561;SizeDiff=4;StartDistance=57;EndDistance=57;GTMatch=.;TruScore=98;MatchId=602.1 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:4,2:6:0,4,0,2 @@ -711,7 +706,6 @@ chr18 79336168 Sniffles2.INS.1E7S11 T TGCCCTCCCTGGCACCAGGCGCTCCCCTCGCCCGTCCCCAGC chr18 79336199 pbsv.INS.1411 C CCGTCCCCAGCACCGCCGTGTGCACCCTCCATGCCCTCCCTGGCACCAGGCGCTCCCCTCGCCCGTCCCCAGCACCGCCGTGTGCACCCTCCATGCCCTCCCTGGCACCAGGTGCTCCCCTCGCCCGTCCCCAGCACCGCCGTGTGCACCCTCCATGCCCTCCCTGGCACCAGGCGCTCCCCTCGCCCGTCCCCAGCACCGCCGTGTGCACCCTCCGTGCCCTCCCTGGCACCAGGTGCTCCCCTCGCCCGTCCCCAGCACCGCCGTGTGCACCCTCCATGCCCTCCCTGGCACCAGGCGCTCCCCTCGCC 2 PASS SVTYPE=INS;SVLEN=310;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9968;PctSizeSimilarity=1;PctRecOverlap=0.8971;SizeDiff=0;StartDistance=-32;EndDistance=-32;GTMatch=.;TruScore=96;MatchId=609.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,9:9:0,0,4,5 chr18 79341280 Sniffles2.DEL.3B2S11 CTGTGTTGCCGACACACCATTTAGTTGTGGTTGGATGTGTGTAGCGTGACCTCGTCGAAGTCTGTGTTGCCGACACACCATTTAGTTGTGGTTGGATGTGTGTAGCGTGACCTCGTTGAAGCC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-122;SUPPORT=7;COVERAGE=7,7,7,7,7;STRAND=+-;AF=1;STDEV_LEN=0.894;STDEV_POS=4.919;AC=2;PctSeqSimilarity=0.9959;PctSizeSimilarity=1;PctRecOverlap=0.9919;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=610.0 GT:GQ:DR:DV ./.:.:.:. 1/1:19:0:7 ./.:.:.:. chr18 79346416 Sniffles2.DEL.3B3S11 GGTCAGCGCACGTCAGCACGTGCTCAGCGCACAGTCAGCACACATTCGGCACACATTTAGCACACTACATGCTTGGCACACACTCAGCGCACCTCAGCATGTGTTCAGTGCACAGTCAGCACACACTCGGCACACACTCG G 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-139;SUPPORT=7;COVERAGE=7,7,7,7,6;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=0.9964;PctSizeSimilarity=1;PctRecOverlap=0.9929;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=611.0 GT:GQ:DR:DV ./.:.:.:. 1/1:19:0:7 ./.:.:.:. -chr18 79357396 pbsv.DEL.1416 GTCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGCCCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTGTCCTGGGTCTGGAGGTGTCCGTGTGAGGGACCCTGTGTGAGGGATGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGACCCTGTGTGAGGGGTGCTCTGGGTCTGGAGGTGTCTGTGTGAGGGGTG G 2 PASS SVTYPE=DEL;SVLEN=-436;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9977;PctSizeSimilarity=1;PctRecOverlap=0.968;SizeDiff=0;StartDistance=-14;EndDistance=-14;GTMatch=.;TruScore=98;MatchId=612.9 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:3,1:4:1,2,0,1 chr18 79385402 Sniffles2.INS.1EDS11 C AGGCCACACCGCCGGGGCCAGGCCACACCGCCGGGGCCAGGCCACACCACCACGG 3 PASS PRECISE;SVTYPE=INS;SVLEN=55;SUPPORT=9;COVERAGE=10,10,10,10,10;STRAND=+-;AF=0.9;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.991;PctSizeSimilarity=1;PctRecOverlap=0.9818;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=613.0 GT:GQ:DR:DV ./.:.:.:. 1/1:15:1:9 ./.:.:.:. chr18 79400833 Sniffles2.INS.1EES11 C CCCCTCCCCCGACCTCCCCCCCGCGCCCCGACCTCCTCCCTGTTCCCTCCCCCGACCTCCCCCTTCCCCCCCGACCTACACCCCGCCCCCCTACCTCCCCCCTCCCCGTGACCTGGCCCCCCAGAACTCCTCCCCATCCCGCCCCCCGACCTCCCCCCGGCCCCCCTCCCCCGG 3 PASS PRECISE;SVTYPE=INS;SVLEN=174;SUPPORT=6;COVERAGE=5,5,6,6,6;STRAND=+-;AF=1;STDEV_LEN=1.5;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9914;PctSizeSimilarity=0.9885;PctRecOverlap=0.9886;SizeDiff=-2;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=614.0 GT:GQ:DR:DV ./.:.:.:. 1/1:16:0:6 ./.:.:.:. chr18 79408993 Sniffles2.DEL.3B8S11 TTCCTCCATTCCCTATCCATCCGTCCATCCATCATCCATCCATCATCATCCATCCATTATTCCTCCATTCCCTATCCATTCATTCATCATCCATCCATCCATCATCATCCATCCATCCATCAAACCATTATTCCTCCATTCCCTATCCATCCATCCGTCATCCATCTATCCATCATCATCCATCCATCATCAAACCATTGT T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-200;SUPPORT=7;COVERAGE=7,7,7,7,6;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=0.9975;PctSizeSimilarity=1;PctRecOverlap=0.995;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=615.0 GT:GQ:DR:DV ./.:.:.:. 1/1:19:0:7 ./.:.:.:. @@ -728,7 +722,6 @@ chr18 79584087 Sniffles2.INS.1FCS11 C CCCCCCCCCGGGTGCTCCTGGGCGTGGGCAGGGCGTGCCCCC chr18 79617323 Sniffles2.INS.1FES11 C CCCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCCGCCCCCCCAGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGACCCCCGCCCCCCCGGGACCCCGCCCCCCCCGGGACCCCGCCCCCCCGGGATGCCGCCCTCCCCGGGACCCCGCCCCCCGGGACCCCGCCCTCCCCGGACCCCGCCCCCCGGGACCCCCGCCCTCCCCGGGACCCCGCCCCCCCAGGACCCCGCCCCCCCAGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGAC 3 PASS PRECISE;SVTYPE=INS;SVLEN=274;SUPPORT=3;COVERAGE=7,7,7,7,7;STRAND=+-;AF=0.429;STDEV_LEN=3.215;STDEV_POS=4.619;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9856;PctSizeSimilarity=1;PctRecOverlap=0.9673;SizeDiff=0;StartDistance=-9;EndDistance=-9;GTMatch=.;TruScore=98;MatchId=629.0 GT:GQ:DR:DV ./.:.:.:. 0/1:18:4:3 ./.:.:.:. chr18 79617366 pbsv.INS.1443 C CAGGACCCCGCCCTCCCCGGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCGCCCCCCCAGGACCCCCGCCCCCC 2 PASS SVTYPE=INS;SVLEN=97;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9847;PctSizeSimilarity=1;PctRecOverlap=0.9691;SizeDiff=0;StartDistance=3;EndDistance=3;GTMatch=.;TruScore=98;MatchId=629.1 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:3,4:7:2,1,2,2 chr18 79617370 Sniffles2.INS.1FDS11 A ACCCCGCCCTCCCCGGGACCCCCGCCCCCCTGTATGCCGCCCTCCCCGGGACCCCGCCCCCCAGGACCCCGCCCCCCCCAGGACCCCCGCCCCCCTGT 3 PASS PRECISE;SVTYPE=INS;SVLEN=98;SUPPORT=4;COVERAGE=7,7,7,7,7;STRAND=+-;AF=0.571;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9898;PctSizeSimilarity=0.9898;PctRecOverlap=0.9798;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=629.1 GT:GQ:DR:DV ./.:.:.:. 0/1:18:3:4 ./.:.:.:. -chr18 79619105 pbsv.DEL.1446 CCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGACGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACATTGTGTGAAATCAGTGTGAGCACACTGTTTACATGCTAACAGGATCACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCACACTGTTTACATGCTAACAGGACCACAGCAGACACTGTGTGAAATCAGTCAGTGCGAGCACACTGTTTACACGCTAACAGGATGACAGCAGACACTGTGTGAAATCAGTCAGTGTGAGCCCACTGTTTACATGCTAACAGGAT C 2 PASS SVTYPE=DEL;SVLEN=-828;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9795;PctSizeSimilarity=0.9952;PctRecOverlap=0.3709;SizeDiff=4;StartDistance=-524;EndDistance=-520;GTMatch=.;TruScore=78;MatchId=630.6 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:8,1:9:4,4,0,1 chr18 79620747 Sniffles2.INS.203S11 A ACACTGTTTAGAAACACAGATGGAGACAGCTGGAGCGTGTGTGGACGTGGACACTGTTTAGAAACACAGATGGAGACAGCTGGAGCGTGTGTGGAGGTGGAGACTGTTTAGAAACACAGATGGAGACAGCTGGAGCGTGTGTGGAGGTGG 3 PASS PRECISE;SVTYPE=INS;SVLEN=150;SUPPORT=2;COVERAGE=8,6,6,6,6;STRAND=+-;AF=0.333;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9967;PctSizeSimilarity=1;PctRecOverlap=0.9934;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=630.3 GT:GQ:DR:DV ./.:.:.:. 0/1:8:4:2 ./.:.:.:. chr18 79622766 Sniffles2.INS.204S11 T TTGGTTTGGTGTGAAGACCCCACCCATTCAATGTAATTTATTAAAGGTCATTTTCTTCTACTGCAATGAACCCAGCA 3 PASS PRECISE;SVTYPE=INS;SVLEN=77;SUPPORT=2;COVERAGE=6,6,6,6,6;STRAND=+-;AF=0.333;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9935;PctSizeSimilarity=1;PctRecOverlap=0.987;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=631.1 GT:GQ:DR:DV ./.:.:.:. 0/1:8:4:2 ./.:.:.:. chr18 79622766 Sniffles2.DEL.3C2S11 TTGGTTTGGTGTGAAGACCCCACCCATTCAATGTAATTTATTAAAGGTCATTTTCTTCTACTGCAATGAACCCAGCAT T 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-77;SUPPORT=4;COVERAGE=6,6,6,6,6;STRAND=+-;AF=0.667;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=0.9936;PctSizeSimilarity=1;PctRecOverlap=0.9872;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=631.0 GT:GQ:DR:DV ./.:.:.:. 0/1:8:2:4 ./.:.:.:. @@ -746,7 +739,6 @@ chr18 79726895 pbsv.INS.1471 A ACGTCTGTGGGGTATGGGTTGATGCCGTTGCTGGTGGACTGCTGTGGGG chr18 79726898 Sniffles2.INS.212S11 G TCTGTGGGGTATGGGGTTGATGCCGTTGCTGGTGGACTGCTGTGGGGGTGGGGTGACGCCGTTGCTGGTGGACGTCTGTGGGGTATGGGGTTGATGCCGTTGCTGGTGGACT 3 GT PRECISE;SVTYPE=INS;SVLEN=112;SUPPORT=2;COVERAGE=7,8,8,8,9;STRAND=+;AF=0.25;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9956;PctSizeSimilarity=1;PctRecOverlap=0.9912;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=638.0 GT:GQ:DR:DV ./.:.:.:. 0/1:3:6:2 ./.:.:.:. chr18 79739802 Sniffles2.DEL.3C4S11 GGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACGGCCGGGACGGGTGGGACTCTCATACCCACG G 0 PASS IMPRECISE;SVTYPE=DEL;SVLEN=-330;SUPPORT=7;COVERAGE=7,7,7,7,7;STRAND=+-;AF=1;STDEV_LEN=16.619;STDEV_POS=13.777;AC=2;PctSeqSimilarity=0.997;PctSizeSimilarity=1;PctRecOverlap=0.9215;SizeDiff=0;StartDistance=-26;EndDistance=-26;GTMatch=.;TruScore=97;MatchId=639.1 GT:GQ:DR:DV ./.:.:.:. 1/1:19:0:7 ./.:.:.:. chr18 79745408 Sniffles2.DEL.3C5S11 CCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGGGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTGCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTCCCTCCCGTGCGCGTTCTGTCCCCGCGTC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-391;SUPPORT=4;COVERAGE=4,4,4,4,4;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;AC=2;PctSeqSimilarity=0.9987;PctSizeSimilarity=0.9974;PctRecOverlap=0.9059;SizeDiff=1;StartDistance=-37;EndDistance=-36;GTMatch=.;TruScore=96;MatchId=640.0 GT:GQ:DR:DV ./.:.:.:. 1/1:11:0:4 ./.:.:.:. -chr18 79765504 chr18-79765505-DEL-85 GCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCATAGCCCCAACCCCATGTGTGAGTGACCAGGGTCACCAGCAGCGTA G 4 . ID=chr18-79765505-DEL-85;SVTYPE=DEL;SVLEN=-85;TIG_REGION=h2tg008684l:117580-117580;QUERY_STRAND=+;HOM_REF=0,3;HOM_TIG=0,3;AC=1;PctSeqSimilarity=0.9942;PctSizeSimilarity=0.9884;PctRecOverlap=0;SizeDiff=1;StartDistance=-343;EndDistance=-342;GTMatch=.;TruScore=66;MatchId=641.1 GT 0/1 ./. ./. chr18 79771157 pbsv.INS.1480 C CACAGGGCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCATGCCAGCCTCCCCTCCACACCGTCCTCCCCTCCATGCCAGCCTCCCCTCCACACCGTCCTCCCCTCCACACAGGGCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACGCCATCCTCCCCTCCACACCGTCCTCCCCTCCACGCCAGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCATGCCAGCCTCCCCTCCATGACATCCTCCCTTCCATGACATCCTCCCCTCCACGGCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACACCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCATCCTCCCCTCCACACAGGGCTCCCCTCCATGCCGTCCTCCCCTCCACACAGGGCTCCCCTCCACGCCAGCCTCCCCTCCATGACATCCTCCCCTCCATGACATCCTCCCTTCCACGCCGTCCTCCCCTCCACACCGGCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCATCCTCCCCTCCACAGCGGCCTCCCCTCCACACTGTCCTCCCCTCCACGCCGTCCTCCCCTCCACGCCAGCCTCCCCTCCATGACATCCTCCCCTCCAT 2 PASS SVTYPE=INS;SVLEN=748;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9775;PctSizeSimilarity=0.9559;PctRecOverlap=0.9506;SizeDiff=-33;StartDistance=20;EndDistance=20;GTMatch=.;TruScore=96;MatchId=642.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:2,3:5:1,1,2,1 chr18 79772466 Sniffles2.INS.219S11 A AGGAGAGGAGGGTCGGGTGCAGGGCCGGGTCCTGTCCTGCTGAGTCCATGGGGAGGTG 3 PASS PRECISE;SVTYPE=INS;SVLEN=58;SUPPORT=4;COVERAGE=5,5,5,5,5;STRAND=+-;AF=0.8;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9915;PctSizeSimilarity=1;PctRecOverlap=0.9831;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=643.0 GT:GQ:DR:DV ./.:.:.:. 1/1:1:1:4 ./.:.:.:. chr18 79780270 Sniffles2.DEL.3CBS11 GGTGCACACTGTCCGCCCTGGACCAGCCAGGACTTTGCTTCCTGCATCTTAGACCCTGCTGACCTCACCCTCCAGAGGCTGCCCTGTGAACATCAGTGCTGGCCGG G 0 PASS IMPRECISE;SVTYPE=DEL;SVLEN=-105;SUPPORT=2;COVERAGE=5,5,5,5,5;STRAND=-;AF=0.4;STDEV_LEN=0.707;STDEV_POS=58.69;AC=1;PctSeqSimilarity=0.9953;PctSizeSimilarity=0.9906;PctRecOverlap=0.9813;SizeDiff=1;StartDistance=-2;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=644.0 GT:GQ:DR:DV ./.:.:.:. 0/1:11:3:2 ./.:.:.:. diff --git a/truvari/collapse.py b/truvari/collapse.py index 437cf01e..9ffdf26b 100644 --- a/truvari/collapse.py +++ b/truvari/collapse.py @@ -107,7 +107,8 @@ def collapse_chunk(chunk, matcher): short_circuit=True) if matcher.hap and not hap_resolve(m_collap.entry, candidate): mat.state = False - if mat.state and matcher.gt and not gt_resolve(m_collap.entry, candidate): + if mat.state and matcher.gt and not gt_compatible(m_collap.entry, candidate): + logging.debug("uncompat GT") mat.state = False if mat.state: m_collap.matches.append(mat) @@ -299,25 +300,15 @@ def hap_resolve(entryA, entryB): return True -def gt_resolve(entryA, entryB): +def gt_compatible(entryA, entryB): """ - Returns true if the calls' genotypes suggest it shouldn't be collapsed + Returns false if the calls' genotypes suggest it shouldn't be collapsed i.e. if both are HOM """ - def compat_phase(a, b): - if None in a or None in b: - return False # nothing preventing it - if a == b: # can't collapse same phase - return True - return False - for sample in entryA.samples: gtA = entryA.samples[sample].allele_indices gtB = entryB.samples[sample].allele_indices - if (gtA == (1, 1) and None not in gtB) \ - or (gtB == (1, 1) and None not in gtA): - return False - if entryA.samples[sample].phased and entryB.samples[sample].phased and compat_phase(gtA, gtB): + if 1 in gtA and 1 in gtB: # present in both, can't merge return False return True @@ -425,7 +416,7 @@ def parse_args(args): parser.add_argument("--bed", type=str, default=None, help="Bed file of regions to analyze") parser.add_argument("--gt", action="store_true", - help="Disallow intra-sample homozygous events to collapse (%(default)s)") + help="Disallow intra-sample events to collapse (%(default)s)") parser.add_argument("--intra", action="store_true", help="Intrasample merge to first sample in output (%(default)s)") parser.add_argument("--median-info", action="store_true",