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updating collapse --gt
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There were edge cases where gt wasn't working. Fixing that problem
exposed involved adding a little more control over what's considered
conflicting genotypes
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@ACEnglish
ACEnglish committed Jan 11, 2024
1 parent fbfba13 commit 0474d15
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Showing 7 changed files with 2,891 additions and 33 deletions.
11 changes: 7 additions & 4 deletions repo_utils/answer_key/collapse/inputintragt_collapsed.vcf
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3 changes: 0 additions & 3 deletions repo_utils/answer_key/collapse/inputintragt_removed.vcf
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Expand Up @@ -598,7 +598,6 @@ chr18 75068025 Sniffles2.DEL.368S11 GAAGATGGCTAAAAGTACGCACAGGGAAGGGGAGCAGGCACTGG
chr18 75104861 Sniffles2.DEL.369S11 GAAGCTCCGTGGAAGCTTGCTGAAATGTCCTGCTTGTGTTTTACTCCGTGGCGAGCACAGCGTGCAGGCGCTCCGTG G 0 GT PRECISE;SVTYPE=DEL;SVLEN=-76;SUPPORT=2;COVERAGE=9,11,11,11,11;STRAND=-;AF=0.182;STDEV_LEN=0.707;STDEV_POS=4.95;AC=0;PctSeqSimilarity=0.9808;PctSizeSimilarity=0.9744;PctRecOverlap=0;SizeDiff=2;StartDistance=161;EndDistance=163;GTMatch=.;TruScore=65;MatchId=510.0 GT:GQ:DR:DV ./.:.:.:. 0/0:5:9:2 ./.:.:.:.
chr18 75105023 Sniffles2.DEL.36AS11 GTGGAAGCTTTGCTGAAATGTCCTGCTTGTGTTTTACTCCGTGGCGAGCACAGCGTGCAGGTGCTCCGTGGAAGCTCAG G 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-78;SUPPORT=3;COVERAGE=10,11,11,11,11;STRAND=+-;AF=0.273;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=0.9937;PctSizeSimilarity=1;PctRecOverlap=0.9873;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=510.0 GT:GQ:DR:DV ./.:.:.:. 0/1:7:8:3 ./.:.:.:.
chr18 75299570 Sniffles2.DEL.36BS11 CAGTGGACGGTGATCCATCGTTAAAGGACATGGTGAGCTTGCACCAGGCACTAGATAGCTGCCCCGCAGTGGACGGTGATCCATCGTTAAAGGACATGGTGAGCTTGCACCAGGCACTAGATAGCTGCCCCGC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-132;SUPPORT=5;COVERAGE=7,7,7,7,7;STRAND=+-;AF=0.714;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=0.9925;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=511.0 GT:GQ:DR:DV ./.:.:.:. 0/1:6:2:5 ./.:.:.:.
chr18 75299831 Sniffles2.DEL.36CS11 CCGCAGTGGACGGTGATCCATCGTTAAAGGACATGGTGAGCTTGCACCAGGCACTAGATAGCTGCCCCGCAGTGGACGGTGATCCATCGTTAAAGGACATGGTGAGCTTGCACCAGGCACTAGATAGCTGCC C 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-131;SUPPORT=2;COVERAGE=7,7,7,7,7;STRAND=+-;AF=0.286;STDEV_LEN=1.414;STDEV_POS=21.92;AC=1;PctSeqSimilarity=0.9925;PctSizeSimilarity=0.9924;PctRecOverlap=0;SizeDiff=1;StartDistance=-262;EndDistance=-261;GTMatch=.;TruScore=66;MatchId=511.0 GT:GQ:DR:DV ./.:.:.:. 0/1:6:5:2 ./.:.:.:.
chr18 75526515 pbsv.INS.1225 C CGGAATGGAAGTACATGGCAAGCTCACGGACCATGGGGGGACACAACCAAGTAGAGTCTGGGGAGGTTGGCTGGACGGGGCTGGGAAATGATAGAATTAGCAGAAACACGAT 2 PASS SVTYPE=INS;SVLEN=111;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.991;PctSizeSimilarity=0.991;PctRecOverlap=0;SizeDiff=-1;StartDistance=170;EndDistance=170;GTMatch=.;TruScore=66;MatchId=512.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:1,3:4:0,1,3,0
chr18 75526686 Sniffles2.INS.16CS11 G GGGAGGTTGGCTGGACGGGGCTGGGAAATGATAGAATTAGCAGAAACACGATGGAATGGAAGTACATGGCAAGCTCACGGACCATGGGGGGACACAACCAAGTAGAGTCT 3 PASS IMPRECISE;SVTYPE=INS;SVLEN=111;SUPPORT=3;COVERAGE=4,4,4,4,4;STRAND=+;AF=0.75;STDEV_LEN=0.577;STDEV_POS=98.15;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=0.9955;PctSizeSimilarity=0.991;PctRecOverlap=0.991;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=512.0 GT:GQ:DR:DV ./.:.:.:. 0/1:1:1:3 ./.:.:.:.
chr18 75712365 pbsv.DEL.1228 CAAAATGGCAGCTGCATGGCTGACTCTCAGATCCAAAATGGCTGCTGCATGGCCGACTCTCTCAGATCC C 2 PASS SVTYPE=DEL;SVLEN=-68;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9855;PctSizeSimilarity=1;PctRecOverlap=0.7971;SizeDiff=0;StartDistance=-14;EndDistance=-14;GTMatch=.;TruScore=92;MatchId=513.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:4,2:6:1,3,2,0
Expand Down Expand Up @@ -669,15 +668,13 @@ chr18 78504366 Sniffles2.DEL.396S11 CCTGAGGATGCCAGCCCGACAGAGCACGGTGTCGGCCAGGAGGA
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 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 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 ./.:.:.:.
chr18 78583487 Sniffles2.INS.1BDS11 C TCTGTCTCCAGCCTCATGTTCCTGAGGCCTGTGGGGTTTTCTCTCTCCAGCCTCGTGCTCCTGAGGCCTGTGGGGTTTTCTCTCTCCAGCCCCGTGCTCCTGAGGCCTGTGGGGTTTC 3 PASS PRECISE;SVTYPE=INS;SVLEN=118;SUPPORT=3;COVERAGE=8,8,8,9,9;STRAND=+-;AF=0.375;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;AC=1;PctSeqSimilarity=1;PctSizeSimilarity=0.9915;PctRecOverlap=0.9832;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=580.0 GT:GQ:DR:DV ./.:.:.:. 0/1:16:5:3 ./.:.:.:.
chr18 78584620 Sniffles2.DEL.397S11 GCCTCCTCTCTGAGCCTCCCTTTCGCCTCGTGTGCTGAGCAGGCGTGGGCAGAGGCCACAGTGAGCAGACGG G 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-71;SUPPORT=3;COVERAGE=9,9,9,9,8;STRAND=+-;AF=0.333;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=0.9931;PctSizeSimilarity=1;PctRecOverlap=0.9861;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=581.0 GT:GQ:DR:DV ./.:.:.:. 0/1:13:6:3 ./.:.:.:.
chr18 78584624 pbsv.DEL.1365 CCTCTCTGAGCCTCCCTTTCGCCTCGTGTGCTGAGCAGGCGTGGGCAGAGGCCACAGTGAGCAGACGGCCTC C 2 PASS SVTYPE=DEL;SVLEN=-71;SVANN=TANDEM;AC=1;PctSeqSimilarity=0.9861;PctSizeSimilarity=1;PctRecOverlap=0.9306;SizeDiff=0;StartDistance=-5;EndDistance=-5;GTMatch=.;TruScore=97;MatchId=581.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 0/1:6,3:9:4,2,2,1
chr18 78613602 pbsv.DEL.1368 TACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTGTAGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATATACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTGTAGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTGTAGGTGGGATACACTCCCTCACTGGGTGTAGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGAC T 2 PASS SVTYPE=DEL;SVLEN=-672;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9851;PctSizeSimilarity=1;PctRecOverlap=0.581;SizeDiff=0;StartDistance=282;EndDistance=282;GTMatch=.;TruScore=85;MatchId=583.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:0,7:7:0,0,2,5
chr18 78613881 pbsv.DEL.1369 ATACACTCCCTCACTGGGTGTAGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTGTGGGTGGGATATACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACAATCCTTCACTGGGTGTGGGTGGGATATACTCCCTCACTGGATGTGGGTGGGA A 2 PASS SVTYPE=DEL;SVLEN=-672;SVANN=TANDEM;AC=2;PctSeqSimilarity=0.9978;PctSizeSimilarity=1;PctRecOverlap=0.9955;SizeDiff=0;StartDistance=3;EndDistance=3;GTMatch=.;TruScore=99;MatchId=583.0 GT:AD:DP:SAC ./.:.:.:. ./.:.:.:. 1/1:1,7:8:1,0,2,5
chr18 78613913 Sniffles2.DEL.39BS11 ACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTATGGGTGGGATACACTCCCTCACTGGGTGTGGGTGGGATATACTCCCTCACTGGGTGTGGGTGGGACACACTCCCTCACTGGGTGTGGGTGGGACACAATCCTTCACTGGGTGTGGGTGGGATATACTCCCTCACTGGATGTGGGTGGGATGTA A 0 PASS PRECISE;SVTYPE=DEL;SVLEN=-644;SUPPORT=4;COVERAGE=7,7,7,7,8;STRAND=+-;AF=0.571;STDEV_LEN=0;STDEV_POS=0;AC=1;PctSeqSimilarity=0.9788;PctSizeSimilarity=0.9583;PctRecOverlap=0.9569;SizeDiff=28;StartDistance=-29;EndDistance=-1;GTMatch=.;TruScore=96;MatchId=583.0 GT:GQ:DR:DV ./.:.:.:. 0/1:18:3:4 ./.:.:.:.
chr18 78645366 Sniffles2.INS.1BES11 G GGCGGCGAGACCACACGTCCACACCAGGCCCAGACCTCAGCGCCTCGGGGGCGGGCGGCGAGACCACACGTCCACACCAGGCCCAGACCTCAGCGCCTCGGGGGCG 3 PASS PRECISE;SVTYPE=INS;SVLEN=106;SUPPORT=9;COVERAGE=8,9,9,9,9;STRAND=+-;AF=1;STDEV_LEN=0.894;STDEV_POS=18.783;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9953;PctSizeSimilarity=1;PctRecOverlap=0.9907;SizeDiff=0;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=99;MatchId=585.0 GT:GQ:DR:DV ./.:.:.:. 1/1:25:0:9 ./.:.:.:.
chr18 78651489 Sniffles2.INS.1BFS11 G GGGGGGCACCTGTGTGCACAACCCTGAGGACGGGACTGCAGGGCCAGAGGGCGCGTGC 3 PASS PRECISE;SVTYPE=INS;SVLEN=58;SUPPORT=6;COVERAGE=7,6,6,6,6;STRAND=+-;AF=1;STDEV_LEN=0.5;STDEV_POS=0;SUPPORT_LONG=0;AC=2;PctSeqSimilarity=0.9914;PctSizeSimilarity=0.9828;PctRecOverlap=0.9661;SizeDiff=-1;StartDistance=-1;EndDistance=-1;GTMatch=.;TruScore=98;MatchId=586.0 GT:GQ:DR:DV ./.:.:.:. 1/1:16:0:6 ./.:.:.:.
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