diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java index 4d47875d47b..a33b5c354e3 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java @@ -109,12 +109,13 @@ public AlleleLikelihoods computeReadLikelihoods(final List< @Override public ToDoubleFunction log10MinTrueLikelihood(final double expectedErrorRate, final boolean capLikelihoods) { final double log10ErrorRate = Math.log10(expectedErrorRate); - final double catastrophicErrorRate = Math.log10(fbargs.fillingValue); - + final double catastrophicErrorRate = fbargs.fillingValue; + final double log10catastrophicErrorRate = Math.log10(fbargs.fillingValue); return read -> { final double maxErrorsForRead = capLikelihoods ? Math.max(MAX_ERRORS_FOR_READ_CAP, Math.ceil(read.getLength() * expectedErrorRate)) : Math.ceil(read.getLength() * expectedErrorRate); - final double maxCatastrophicErrorsForRead = capLikelihoods ? Math.max(MAX_CATASTROPHIC_ERRORS_FOR_READ_CAP, Math.ceil(read.getLength() * catastrophicErrorRate)) : Math.ceil(read.getLength() * catastrophicErrorRate); - return maxErrorsForRead * log10ErrorRate + maxCatastrophicErrorsForRead * catastrophicErrorRate; + final double maxCatastrophicErrorsForRead = capLikelihoods ? Math.max(MAX_CATASTROPHIC_ERRORS_FOR_READ_CAP, Math.ceil(read.getLength() * fbargs.fillingValue)) : + Math.ceil(read.getLength() * fbargs.fillingValue); + return maxErrorsForRead * log10ErrorRate + maxCatastrophicErrorsForRead * log10catastrophicErrorRate; }; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedHMMEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedHMMEngine.java index 9af6c6a1311..f4b5726e600 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedHMMEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedHMMEngine.java @@ -124,7 +124,7 @@ public ToDoubleFunction log10MinTrueLikelihood(final double expectedEr return read -> { final double maxErrorsForRead = Math.max(3.0, Math.ceil(read.getLength() * expectedErrorRate)); - final double maxCatastrophicErrorsForRead = Math.max(2.0, Math.ceil(read.getLength() * catastrophicErrorRate)); + final double maxCatastrophicErrorsForRead = Math.max(2.0, Math.ceil(read.getLength() * fbargs.fillingValue)); return maxErrorsForRead * log10ErrorRate + maxCatastrophicErrorsForRead*catastrophicErrorRate; }; } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf index d68a2e3109a..309061d6bb7 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf @@ -3859,7 +3859,7 @@ chr9 81151898 . G . . END=81151898 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,9 chr9 81151899 . G . . END=81151974 GT:DP:GQ:MIN_DP:PL 0/0:50:99:45:0,106,1800 chr9 81151975 . G . . END=81151975 GT:DP:GQ:MIN_DP:PL 0/0:49:85:49:0,85,1477 chr9 81151976 . G . . END=81152018 GT:DP:GQ:MIN_DP:PL 0/0:51:99:48:0,118,1800 -chr9 81152019 . T A, 67.64 . ASSEMBLED_HAPS=2;BaseQRankSum=-0.939;DP=49;ExcessHet=0.0000;FILTERED_HAPS=0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=-1.630 GT:AD:DP:GQ:PL:SB 0/1:24,25,0:49:40:75,0,40,1050,1008,1083:14,10,19,6 +chr9 81152019 . T A, 67.64 . ASSEMBLED_HAPS=2;BaseQRankSum=-0.939;DP=50;ExcessHet=0.0000;FILTERED_HAPS=0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=180000,50;ReadPosRankSum=-1.630 GT:AD:DP:GQ:PL:SB 0/1:24,25,0:49:40:75,0,40,1050,1008,1083:14,10,19,6 chr9 81152020 . G . . END=81152065 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,112,1800 chr9 81152066 . C . . END=81152066 GT:DP:GQ:MIN_DP:PL 0/0:51:64:51:0,64,2104 chr9 81152067 . T . . END=81152098 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,117,1724 @@ -5430,10 +5430,8 @@ chr9 81162397 . C . . END=81162397 GT:DP:GQ:MIN_DP:PL 0/0:44:98:44:0,9 chr9 81162398 . A . . END=81162403 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,107,1800 chr9 81162404 . A . . END=81162404 GT:DP:GQ:MIN_DP:PL 0/0:45:91:45:0,91,1882 chr9 81162405 . C . . END=81162430 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800 -chr9 81162431 . G C, 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-1.085;DP=47;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=169200,47;ReadPosRankSum=-1.179;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:43,3,0:46:42:0|1:81162431_G_C:0,42,82,129,1802,169:81162431:22,21,0,3 -chr9 81162432 . G . . END=81162432 GT:DP:GQ:MIN_DP:PL 0/0:45:99:45:0,120,1800 -chr9 81162433 . A AG, 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-2.096;DP=47;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=169200,47;ReadPosRankSum=-1.248;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:42,4,0:46:13:0|1:81162431_G_C:0,13,53,122,918,162:81162431:22,20,0,4 -chr9 81162434 . G . . END=81162477 GT:DP:GQ:MIN_DP:PL 0/0:45:99:43:0,101,1731 +chr9 81162431 . G . . END=81162431 GT:DP:GQ:MIN_DP:PL 0/0:51:59:51:0,59,1437 +chr9 81162432 . G . . END=81162477 GT:DP:GQ:MIN_DP:PL 0/0:49:99:47:0,105,1800 chr9 81162478 . C . . END=81162479 GT:DP:GQ:MIN_DP:PL 0/0:47:97:47:0,97,1928 chr9 81162480 . A . . END=81162487 GT:DP:GQ:MIN_DP:PL 0/0:46:99:45:0,105,1494 chr9 81162488 . T . . END=81162488 GT:DP:GQ:MIN_DP:PL 0/0:45:91:45:0,91,1496 @@ -6896,7 +6894,7 @@ chr9 81173332 . T . . END=81173332 GT:DP:GQ:MIN_DP:PL 0/0:27:62:27:0,6 chr9 81173333 . C . . END=81173338 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 chr9 81173339 . A . . END=81173339 GT:DP:GQ:MIN_DP:PL 0/0:27:36:27:0,36,1094 chr9 81173340 . T . . END=81173368 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,1209 -chr9 81173369 . A G, 67.64 . ASSEMBLED_HAPS=2;BaseQRankSum=-0.472;DP=28;ExcessHet=0.0000;FILTERED_HAPS=0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=100800,28;ReadPosRankSum=0.645 GT:AD:DP:GQ:PL:SB 0/1:13,15,0:28:40:75,0,40,623,546,621:3,10,6,9 +chr9 81173369 . A G, 67.64 . ASSEMBLED_HAPS=2;BaseQRankSum=-0.537;DP=29;ExcessHet=0.0000;FILTERED_HAPS=0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.939 GT:AD:DP:GQ:PL:SB 0/1:14,15,0:29:40:75,0,40,623,588,663:3,11,6,9 chr9 81173370 . G . . END=81173384 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1190 chr9 81173385 . C . . END=81173389 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 chr9 81173390 . A . . END=81173396 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1124 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf.idx index 16313fc31fd..3d4baa9911b 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf index b88f01891ff..e543a043c9c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf @@ -3692,7 +3692,7 @@ chr9 81151866 . A . . END=81151866 GT:DP:GQ:MIN_DP:PL 0/0:44:88:44:0,8 chr9 81151867 . C . . END=81151974 GT:DP:GQ:MIN_DP:PL 0/0:49:94:43:0,94,1800 chr9 81151975 . G . . END=81151975 GT:DP:GQ:MIN_DP:PL 0/0:49:85:49:0,85,1477 chr9 81151976 . G . . END=81152018 GT:DP:GQ:MIN_DP:PL 0/0:51:99:48:0,118,1800 -chr9 81152019 . T A, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-1.0,1|NaN;AS_RAW_MQ=86400.00|90000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|NaN;AS_SB_TABLE=14,10|19,6|0,0;BaseQRankSum=-0.939;DP=49;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=51;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=-1.630 GT:AD:DP:GQ:PL:SB 0/1:24,25,0:49:40:75,0,40,1050,1008,1083:14,10,19,6 +chr9 81152019 . T A, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-1.0,1|NaN;AS_RAW_MQ=86400.00|90000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|NaN;AS_SB_TABLE=14,10|19,6|0,0;BaseQRankSum=-0.939;DP=50;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=53;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=180000,50;ReadPosRankSum=-1.630 GT:AD:DP:GQ:PL:SB 0/1:24,25,0:49:40:75,0,40,1050,1008,1083:14,10,19,6 chr9 81152020 . G . . END=81152065 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,112,1800 chr9 81152066 . C . . END=81152066 GT:DP:GQ:MIN_DP:PL 0/0:51:64:51:0,64,2104 chr9 81152067 . T . . END=81152139 GT:DP:GQ:MIN_DP:PL 0/0:44:95:41:0,95,1724 @@ -3759,7 +3759,7 @@ chr9 81152604 . C . . END=81152612 GT:DP:GQ:MIN_DP:PL 0/0:31:90:31:0,9 chr9 81152613 . T . . END=81152637 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1132 chr9 81152638 . T . . END=81152638 GT:DP:GQ:MIN_DP:PL 0/0:29:78:29:0,78,1170 chr9 81152639 . A . . END=81152646 GT:DP:GQ:MIN_DP:PL 0/0:29:81:29:0,81,1215 -chr9 81152647 . A T, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|68400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=3,6|10,9|0,0;BaseQRankSum=0.000;DP=29;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=29;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.787 GT:AD:DP:GQ:PL:SB 0/1:9,19,0:28:32:75,0,32,783,378,453:3,6,10,9 +chr9 81152647 . A T, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|68400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=3,6|10,9|0,0;BaseQRankSum=0.000;DP=29;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=30;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.787 GT:AD:DP:GQ:PL:SB 0/1:9,19,0:28:32:75,0,32,783,378,453:3,6,10,9 chr9 81152648 . T . . END=81152667 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1156 chr9 81152668 . C . . END=81152675 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,1062 chr9 81152676 . T . . END=81152678 GT:DP:GQ:MIN_DP:PL 0/0:30:87:30:0,87,1305 @@ -4048,7 +4048,7 @@ chr9 81155390 . T . . END=81155455 GT:DP:GQ:MIN_DP:PL 0/0:36:93:31:0,9 chr9 81155456 . C . . END=81155456 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 chr9 81155457 . A . . END=81155457 GT:DP:GQ:MIN_DP:PL 0/0:28:73:28:0,73,860 chr9 81155458 . A . . END=81155467 GT:DP:GQ:MIN_DP:PL 0/0:30:84:28:0,84,926 -chr9 81155468 . A AG, 19.60 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=79200.00|25200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=6,16|7,0|0,0;BaseQRankSum=0.713;DP=30;ExcessHet=0.0000;FILTERED_HAPS=2;HAPCOMP=0,0;HAPDOM=0.857,0.00;HEC=49,1,1;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=108000,30;ReadPosRankSum=1.478;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:22,7,0:29:27:27,0,40,109,523,149:6,16,7,0 +chr9 81155468 . A AG, 19.60 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=79200.00|25200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=6,16|7,0|0,0;BaseQRankSum=0.713;DP=30;ExcessHet=0.0000;FILTERED_HAPS=2;HAPCOMP=0,0;HAPDOM=0.857,0.00;HEC=50,1,1;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=108000,30;ReadPosRankSum=1.478;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:22,7,0:29:27:27,0,40,109,523,149:6,16,7,0 chr9 81155469 . G . . END=81155476 GT:DP:GQ:MIN_DP:PL 0/0:28:75:26:0,75,854 chr9 81155477 . C . . END=81155478 GT:DP:GQ:MIN_DP:PL 0/0:32:61:32:0,61,1031 chr9 81155479 . A . . END=81155479 GT:DP:GQ:MIN_DP:PL 0/0:31:75:31:0,75,1301 @@ -4248,14 +4248,14 @@ chr9 81156483 . A . . END=81156483 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,5 chr9 81156484 . G . . END=81156487 GT:DP:GQ:MIN_DP:PL 0/0:22:63:21:0,63,901 chr9 81156488 . G . . END=81156489 GT:DP:GQ:MIN_DP:PL 0/0:24:72:24:0,72,990 chr9 81156490 . G . . END=81156490 GT:DP:GQ:MIN_DP:PL 0/0:24:69:24:0,69,1035 -chr9 81156491 . T TA, 79.96 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|25200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,5|0,0;DP=23;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=0,0;HAPDOM=0.571,0.00;HEC=35,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=82800,23;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,7,0:7:19:0|1:81156491_T_TA:94,19,0,147,19,94:81156491:0,0,2,5 +chr9 81156491 . T TA, 79.96 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|25200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,5|0,0;DP=23;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=0,0;HAPDOM=0.571,0.00;HEC=37,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=82800,23;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,7,0:7:19:0|1:81156491_T_TA:94,19,0,147,19,94:81156491:0,0,2,5 chr9 81156492 . A . . END=81156492 GT:DP:GQ:MIN_DP:PL 0/0:17:37:17:0,37,292 chr9 81156493 . A . . END=81156493 GT:DP:GQ:MIN_DP:PL 0/0:19:56:19:0,56,464 chr9 81156494 . A . . END=81156501 GT:DP:GQ:MIN_DP:PL 0/0:23:68:23:0,68,510 chr9 81156502 . A . . END=81156502 GT:DP:GQ:MIN_DP:PL 0/0:17:48:17:0,48,241 chr9 81156503 . G . . END=81156505 GT:DP:GQ:MIN_DP:PL 0/0:23:66:23:0,66,803 chr9 81156506 . T . . END=81156509 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,845 -chr9 81156510 . AT A, 7.56 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=79200.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=14,8|0,3|0,0;BaseQRankSum=-1.057;DP=25;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=1,0;HAPDOM=1.00,0.00;HEC=31,7,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=90000,25;ReadPosRankSum=-0.795;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:22,3,0:25:15:0|1:81156491_T_TA:15,0,40,81,593,121:81156491:14,8,0,3 +chr9 81156510 . AT A, 7.56 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=79200.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=14,8|0,3|0,0;BaseQRankSum=-1.057;DP=25;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=1,0;HAPDOM=1.00,0.00;HEC=33,7,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=90000,25;ReadPosRankSum=-0.795;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:22,3,0:25:15:0|1:81156491_T_TA:15,0,40,81,593,121:81156491:14,8,0,3 chr9 81156512 . C . . END=81156512 GT:DP:GQ:MIN_DP:PL 0/0:27:36:27:0,36,1104 chr9 81156513 . C . . END=81156536 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1191 chr9 81156537 . A . . END=81156539 GT:DP:GQ:MIN_DP:PL 0/0:30:90:30:0,90,1274 @@ -4295,7 +4295,7 @@ chr9 81156988 . T . . END=81156988 GT:DP:GQ:MIN_DP:PL 0/0:41:79:41:0,7 chr9 81156989 . A . . END=81157067 GT:DP:GQ:MIN_DP:PL 0/0:46:99:40:0,100,1553 chr9 81157068 . C . . END=81157068 GT:DP:GQ:MIN_DP:PL 0/0:52:66:52:0,66,1938 chr9 81157069 . C . . END=81157097 GT:DP:GQ:MIN_DP:PL 0/0:51:99:45:0,106,1800 -chr9 81157098 . T TG, 13.59 . ASSEMBLED_HAPS=5;AS_RAW_BaseQRankSum=|-1.5,1|NaN;AS_RAW_MQ=115200.00|46800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=14,18|12,1|0,0;BaseQRankSum=-1.447;DP=49;ExcessHet=0.0000;FILTERED_HAPS=3;HAPCOMP=0,0;HAPDOM=0.769,0.00;HEC=65,5,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=-0.150;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:32,13,0:45:21:21,0,40,135,666,175:14,18,12,1 +chr9 81157098 . T TG, 13.59 . ASSEMBLED_HAPS=5;AS_RAW_BaseQRankSum=|-1.5,1|NaN;AS_RAW_MQ=115200.00|46800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=14,18|12,1|0,0;BaseQRankSum=-1.447;DP=49;ExcessHet=0.0000;FILTERED_HAPS=3;HAPCOMP=0,0;HAPDOM=0.769,0.00;HEC=66,5,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=-0.150;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:32,13,0:45:21:21,0,40,135,666,175:14,18,12,1 chr9 81157099 . G . . END=81157112 GT:DP:GQ:MIN_DP:PL 0/0:48:99:43:0,112,1417 chr9 81157113 . G . . END=81157113 GT:DP:GQ:MIN_DP:PL 0/0:46:82:46:0,82,1254 chr9 81157114 . G . . END=81157822 GT:DP:GQ:MIN_DP:PL 0/0:55:92:42:0,92,1601 @@ -4408,16 +4408,16 @@ chr9 81158617 . A . . END=81158617 GT:DP:GQ:MIN_DP:PL 0/0:11:9:11:0,9, chr9 81158618 . T . . END=81158618 GT:DP:GQ:MIN_DP:PL 0/0:10:10:10:0,10,383 chr9 81158619 . G . . END=81158621 GT:DP:GQ:MIN_DP:PL 0/0:9:27:9:0,27,377 chr9 81158622 . C . . END=81158647 GT:DP:GQ:MIN_DP:PL 0/0:12:30:10:0,30,415 -chr9 81158648 . G GA, 0.08 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=5,4|2,0|0,0;BaseQRankSum=0.000;DP=13;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=1,0;HAPDOM=0.500,0.00;HEC=11,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=46800,13;ReadPosRankSum=-0.447;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:9,2,0:11:4:4,0,40,30,186,70:5,4,2,0 +chr9 81158648 . G GA, 0.08 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=5,4|2,0|0,0;BaseQRankSum=0.000;DP=13;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=1,0;HAPDOM=0.500,0.00;HEC=12,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=46800,13;ReadPosRankSum=-0.447;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:9,2,0:11:4:4,0,40,30,186,70:5,4,2,0 chr9 81158649 . A . . END=81158655 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,368 chr9 81158656 . A . . END=81158656 GT:DP:GQ:MIN_DP:PL 0/0:12:21:12:0,21,461 chr9 81158657 . C . . END=81158670 GT:DP:GQ:MIN_DP:PL 0/0:13:31:12:0,31,495 chr9 81158671 . T . . END=81158678 GT:DP:GQ:MIN_DP:PL 0/0:15:42:14:0,42,541 chr9 81158679 . C . . END=81158689 GT:DP:GQ:MIN_DP:PL 0/0:14:36:13:0,36,540 -chr9 81158690 . C CT, 100.02 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|46800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|10,3|0,0;DP=14;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=2,0;HAPDOM=0.538,0.00;HEC=11,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=50400,14 GT:AD:DP:GQ:PL:SB 1/1:0,13,0:13:39:114,39,0,388,39,114:0,0,10,3 +chr9 81158690 . C CT, 100.02 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|46800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|10,3|0,0;DP=14;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=2,0;HAPDOM=0.538,0.00;HEC=12,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=50400,14 GT:AD:DP:GQ:PL:SB 1/1:0,13,0:13:39:114,39,0,388,39,114:0,0,10,3 chr9 81158691 . G . . END=81158693 GT:DP:GQ:MIN_DP:PL 0/0:13:39:13:0,39,549 chr9 81158694 . T . . END=81158711 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,553 -chr9 81158712 . A G, 67.64 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=25200.00|25200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=7,0|4,3|0,0;BaseQRankSum=0.674;DP=14;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=2,0;HAPDOM=1.00,0.00;HEC=12,11,2,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=50400,14;ReadPosRankSum=-1.190 GT:AD:DP:GQ:PL:SB 0/1:7,7,0:14:31:75,0,31,294,294,334:7,0,4,3 +chr9 81158712 . A G, 67.64 . ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=25200.00|25200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=7,0|4,3|0,0;BaseQRankSum=0.674;DP=14;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=2,0;HAPDOM=1.00,0.00;HEC=12,12,2,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=50400,14;ReadPosRankSum=-1.190 GT:AD:DP:GQ:PL:SB 0/1:7,7,0:14:31:75,0,31,294,294,334:7,0,4,3 chr9 81158713 . A . . END=81158738 GT:DP:GQ:MIN_DP:PL 0/0:16:45:16:0,45,663 chr9 81158739 . A . . END=81158759 GT:DP:GQ:MIN_DP:PL 0/0:18:51:17:0,51,730 chr9 81158760 . C . . END=81158760 GT:DP:GQ:MIN_DP:PL 0/0:18:24:18:0,24,731 @@ -4458,9 +4458,9 @@ chr9 81159087 . A . . END=81159087 GT:DP:GQ:MIN_DP:PL 0/0:12:27:12:0,2 chr9 81159088 . G . . END=81159088 GT:DP:GQ:MIN_DP:PL 0/0:13:4:13:0,4,502 chr9 81159089 . C . . END=81159091 GT:DP:GQ:MIN_DP:PL 0/0:12:30:12:0,30,450 chr9 81159092 . G . . END=81159096 GT:DP:GQ:MIN_DP:PL 0/0:11:22:10:0,22,360 -chr9 81159097 . T C, 88.05 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|32400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|5,4|0,0;DP=9;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=2,0;HAPDOM=0.667,0.00;HEC=18,6,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,9,0:9:27:0|1:81159097_T_C:102,27,0,355,27,102:81159097:0,0,5,4 +chr9 81159097 . T C, 88.05 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|32400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|5,4|0,0;DP=9;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=2,0;HAPDOM=0.667,0.00;HEC=19,6,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,9,0:9:27:0|1:81159097_T_C:102,27,0,355,27,102:81159097:0,0,5,4 chr9 81159098 . G . . END=81159101 GT:DP:GQ:MIN_DP:PL 0/0:8:12:8:0,12,180 -chr9 81159102 . C CA, 88.01 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|32400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|5,4|0,0;DP=9;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=2,0;HAPDOM=0.667,0.00;HEC=18,6,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,9,0:9:27:0|1:81159097_T_C:102,27,0,355,27,102:81159097:0,0,5,4 +chr9 81159102 . C CA, 88.01 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|32400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|5,4|0,0;DP=9;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=2,0;HAPDOM=0.667,0.00;HEC=19,6,3;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,9,0:9:27:0|1:81159097_T_C:102,27,0,355,27,102:81159097:0,0,5,4 chr9 81159103 . A . . END=81159112 GT:DP:GQ:MIN_DP:PL 0/0:6:0:4:0,0,0 chr9 81159113 . A . . END=81159113 GT:DP:GQ:MIN_DP:PL 0/0:4:12:4:0,12,95 chr9 81159114 . A . . END=81159115 GT:DP:GQ:MIN_DP:PL 0/0:5:0:5:0,0,53 @@ -4510,7 +4510,7 @@ chr9 81159469 . T . . END=81159469 GT:DP:GQ:MIN_DP:PL 0/0:32:58:32:0,5 chr9 81159470 . T . . END=81159502 GT:DP:GQ:MIN_DP:PL 0/0:40:93:32:0,93,575 chr9 81159503 . T . . END=81159503 GT:DP:GQ:MIN_DP:PL 0/0:39:73:39:0,73,1616 chr9 81159504 . T . . END=81159504 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,111,1665 -chr9 81159505 . G A, 67.64 . ASSEMBLED_HAPS=6;AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=64800.00|79200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=10,8|11,11|0,0;BaseQRankSum=2.774;DP=40;ExcessHet=0.0000;FILTERED_HAPS=4;HAPCOMP=0,0;HAPDOM=0.636,0.00;HEC=49,5,3;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=144000,40;ReadPosRankSum=0.421 GT:AD:DP:GQ:PL:SB 0/1:18,22,0:40:39:75,0,39,880,756,831:10,8,11,11 +chr9 81159505 . G A, 67.64 . ASSEMBLED_HAPS=6;AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=64800.00|79200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=10,8|11,11|0,0;BaseQRankSum=2.774;DP=40;ExcessHet=0.0000;FILTERED_HAPS=4;HAPCOMP=0,0;HAPDOM=0.636,0.00;HEC=51,5,3;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=144000,40;ReadPosRankSum=0.421 GT:AD:DP:GQ:PL:SB 0/1:18,22,0:40:39:75,0,39,880,756,831:10,8,11,11 chr9 81159506 . G . . END=81159586 GT:DP:GQ:MIN_DP:PL 0/0:38:90:34:0,90,1268 chr9 81159587 . A . . END=81159587 GT:DP:GQ:MIN_DP:PL 0/0:37:66:37:0,66,1505 chr9 81159588 . G . . END=81159612 GT:DP:GQ:MIN_DP:PL 0/0:35:93:32:0,93,1395 @@ -4569,7 +4569,7 @@ chr9 81159858 . A . . END=81159858 GT:DP:GQ:MIN_DP:PL 0/0:41:79:41:0,7 chr9 81159859 . C . . END=81159878 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,106,1625 chr9 81159879 . T . . END=81159879 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1791 chr9 81159880 . G . . END=81159969 GT:DP:GQ:MIN_DP:PL 0/0:45:91:40:0,91,1282 -chr9 81159970 . G A, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=61200.00|86400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=5,12|5,19|0,0;BaseQRankSum=0.000;DP=41;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=46;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=147600,41;ReadPosRankSum=-1.390 GT:AD:DP:GQ:PL:SB 0/1:17,24,0:41:37:75,0,37,1008,714,789:5,12,5,19 +chr9 81159970 . G A, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=61200.00|86400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=5,12|5,19|0,0;BaseQRankSum=0.000;DP=41;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=48;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=147600,41;ReadPosRankSum=-1.390 GT:AD:DP:GQ:PL:SB 0/1:17,24,0:41:37:75,0,37,1008,714,789:5,12,5,19 chr9 81159971 . T . . END=81160039 GT:DP:GQ:MIN_DP:PL 0/0:42:99:38:0,99,1290 chr9 81160040 . A . . END=81160040 GT:DP:GQ:MIN_DP:PL 0/0:44:88:44:0,88,1854 chr9 81160041 . T . . END=81160044 GT:DP:GQ:MIN_DP:PL 0/0:44:99:42:0,113,1800 @@ -4737,7 +4737,7 @@ chr9 81161319 . C . . END=81161319 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,8 chr9 81161320 . A . . END=81161327 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,111,1547 chr9 81161328 . G . . END=81161328 GT:DP:GQ:MIN_DP:PL 0/0:39:54:39:0,54,1481 chr9 81161329 . G . . END=81161342 GT:DP:GQ:MIN_DP:PL 0/0:39:99:37:0,103,1574 -chr9 81161343 . T G, 169.06 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|129600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|21,15|0,0;DP=37;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=39;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=133200,37 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:183,108,0,1620,108,183:0,0,21,15 +chr9 81161343 . T G, 169.06 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|129600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|21,15|0,0;DP=37;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=40;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=133200,37 GT:AD:DP:GQ:PL:SB 1/1:0,36,0:36:99:183,108,0,1620,108,183:0,0,21,15 chr9 81161344 . A . . END=81161346 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,117,1755 chr9 81161347 . C . . END=81161347 GT:DP:GQ:MIN_DP:PL 0/0:39:83:39:0,83,1648 chr9 81161348 . A . . END=81161399 GT:DP:GQ:MIN_DP:PL 0/0:42:90:36:0,90,1448 @@ -4835,10 +4835,8 @@ chr9 81162353 . G . . END=81162353 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,8 chr9 81162354 . G . . END=81162377 GT:DP:GQ:MIN_DP:PL 0/0:41:99:41:0,117,1755 chr9 81162378 . T . . END=81162378 GT:DP:GQ:MIN_DP:PL 0/0:41:89:41:0,89,1756 chr9 81162379 . G . . END=81162430 GT:DP:GQ:MIN_DP:PL 0/0:45:91:40:0,91,1732 -chr9 81162431 . G C, 0 . ASSEMBLED_HAPS=14;AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=154800.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=22,21|0,3|0,0;BaseQRankSum=-1.085;DP=47;ExcessHet=0.0000;FILTERED_HAPS=11;HAPCOMP=1,0;HAPDOM=0.500,0.00;HEC=54,3,2,1,1,1,1,0,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=169200,47;ReadPosRankSum=-1.179;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:43,3,0:46:42:0|1:81162431_G_C:0,42,82,129,1802,169:81162431:22,21,0,3 -chr9 81162432 . G . . END=81162432 GT:DP:GQ:MIN_DP:PL 0/0:45:99:45:0,120,1800 -chr9 81162433 . A AG, 0 . ASSEMBLED_HAPS=14;AS_RAW_BaseQRankSum=|-2.1,1|NaN;AS_RAW_MQ=151200.00|14400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=22,20|0,4|0,0;BaseQRankSum=-2.096;DP=47;ExcessHet=0.0000;FILTERED_HAPS=11;HAPCOMP=1,0;HAPDOM=0.400,0.00;HEC=55,2,2,1,1,1,1,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=169200,47;ReadPosRankSum=-1.248;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:42,4,0:46:13:0|1:81162431_G_C:0,13,53,122,918,162:81162431:22,20,0,4 -chr9 81162434 . G . . END=81162503 GT:DP:GQ:MIN_DP:PL 0/0:45:90:43:0,90,1494 +chr9 81162431 . G . . END=81162431 GT:DP:GQ:MIN_DP:PL 0/0:51:59:51:0,59,1437 +chr9 81162432 . G . . END=81162503 GT:DP:GQ:MIN_DP:PL 0/0:48:90:43:0,90,1494 chr9 81162504 . G . . END=81162504 GT:DP:GQ:MIN_DP:PL 0/0:44:88:44:0,88,1671 chr9 81162505 . G . . END=81162581 GT:DP:GQ:MIN_DP:PL 0/0:45:92:39:0,92,1276 chr9 81162582 . T . . END=81162582 GT:DP:GQ:MIN_DP:PL 0/0:40:7:40:0,7,1498 @@ -4961,7 +4959,7 @@ chr9 81164575 . T . . END=81164579 GT:DP:GQ:MIN_DP:PL 0/0:30:81:30:0,8 chr9 81164580 . T . . END=81164591 GT:DP:GQ:MIN_DP:PL 0/0:26:72:25:0,72,1080 chr9 81164592 . A . . END=81164616 GT:DP:GQ:MIN_DP:PL 0/0:21:60:20:0,60,762 chr9 81164617 . T . . END=81164620 GT:DP:GQ:MIN_DP:PL 0/0:19:54:18:0,54,789 -chr9 81164621 . C A, 67.64 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=25200.00|36000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=1,6|3,7|0,0;BaseQRankSum=-0.073;DP=18;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.524,0.00;HEC=33,11,2,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=64800,18;ReadPosRankSum=-0.976 GT:AD:DP:GQ:PL:SB 0/1:7,10,0:17:38:75,0,38,414,255,329:1,6,3,7 +chr9 81164621 . C A, 67.64 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=25200.00|36000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=1,6|3,7|0,0;BaseQRankSum=-0.073;DP=18;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.524,0.00;HEC=34,11,2,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=64800,18;ReadPosRankSum=-0.976 GT:AD:DP:GQ:PL:SB 0/1:7,10,0:17:38:75,0,38,414,255,329:1,6,3,7 chr9 81164622 . A . . END=81164636 GT:DP:GQ:MIN_DP:PL 0/0:16:42:15:0,42,630 chr9 81164637 . T . . END=81164637 GT:DP:GQ:MIN_DP:PL 0/0:17:6:17:0,6,641 chr9 81164638 . C . . END=81164647 GT:DP:GQ:MIN_DP:PL 0/0:16:45:16:0,45,598 @@ -4982,8 +4980,8 @@ chr9 81164682 . C . . END=81164685 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,4 chr9 81164686 . G . . END=81164686 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,761 chr9 81164687 . A . . END=81164687 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,662 chr9 81164688 . C . . END=81164696 GT:DP:GQ:MIN_DP:PL 0/0:19:51:17:0,51,746 -chr9 81164697 . GC G, 28.60 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=54676.00|14400.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=5,11|0,4|0,0;BaseQRankSum=-3.320;DP=21;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.688,0.00;HEC=32,11,2,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.625;RAW_MQandDP=72676,21;ReadPosRankSum=0.473 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,4,0:20:36:0|1:81164697_GC_G:36,0,40,84,614,124:81164697:5,11,0,4 -chr9 81164699 . T A, 28.64 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=54676.00|14400.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=5,11|0,4|0,0;BaseQRankSum=-1.900;DP=21;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.688,0.00;HEC=32,11,2,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.625;RAW_MQandDP=72676,21;ReadPosRankSum=0.520 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,4,0:20:36:0|1:81164697_GC_G:36,0,40,84,614,124:81164697:5,11,0,4 +chr9 81164697 . GC G, 28.60 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=54676.00|14400.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=5,11|0,4|0,0;BaseQRankSum=-3.320;DP=21;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.688,0.00;HEC=33,11,2,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.625;RAW_MQandDP=72676,21;ReadPosRankSum=0.473 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,4,0:20:36:0|1:81164697_GC_G:36,0,40,84,614,124:81164697:5,11,0,4 +chr9 81164699 . T A, 28.64 . ASSEMBLED_HAPS=65;AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=54676.00|14400.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=5,11|0,4|0,0;BaseQRankSum=-1.900;DP=21;ExcessHet=0.0000;FILTERED_HAPS=61;HAPCOMP=3,0;HAPDOM=0.688,0.00;HEC=33,11,2,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.625;RAW_MQandDP=72676,21;ReadPosRankSum=0.520 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,4,0:20:36:0|1:81164697_GC_G:36,0,40,84,614,124:81164697:5,11,0,4 chr9 81164700 . C . . END=81164700 GT:DP:GQ:MIN_DP:PL 0/0:20:60:20:0,60,818 chr9 81164701 . A . . END=81164701 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,663 chr9 81164702 . A . . END=81164703 GT:DP:GQ:MIN_DP:PL 0/0:20:60:20:0,60,785 @@ -5058,7 +5056,7 @@ chr9 81166217 . C . . END=81166217 GT:DP:GQ:MIN_DP:PL 0/0:41:79:41:0,7 chr9 81166218 . A . . END=81166223 GT:DP:GQ:MIN_DP:PL 0/0:40:99:37:0,110,1169 chr9 81166224 . C . . END=81166224 GT:DP:GQ:MIN_DP:PL 0/0:40:86:40:0,86,1656 chr9 81166225 . T . . END=81166243 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,101,1387 -chr9 81166244 . T C, 147.06 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=7200.00|136800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|2.1,1|NaN;AS_SB_TABLE=0,2|21,17|0,0;BaseQRankSum=-1.242;DP=41;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=45,2;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQandDP=147600,41;ReadPosRankSum=2.111;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 1/1:2,38,0:40:86:161,86,0,1677,114,189:0,2,21,17 +chr9 81166244 . T C, 147.06 . ASSEMBLED_HAPS=3;AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=7200.00|136800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|2.1,1|NaN;AS_SB_TABLE=0,2|21,17|0,0;BaseQRankSum=-1.242;DP=41;ExcessHet=0.0000;FILTERED_HAPS=1;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=47,2;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQandDP=147600,41;ReadPosRankSum=2.111;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 1/1:2,38,0:40:86:161,86,0,1677,114,189:0,2,21,17 chr9 81166245 . G . . END=81166259 GT:DP:GQ:MIN_DP:PL 0/0:43:99:40:0,101,1493 chr9 81166260 . A . . END=81166260 GT:DP:GQ:MIN_DP:PL 0/0:43:60:43:0,60,1752 chr9 81166261 . T . . END=81166294 GT:DP:GQ:MIN_DP:PL 0/0:39:92:37:0,92,1363 @@ -5151,7 +5149,7 @@ chr9 81166755 . A . . END=81166755 GT:DP:GQ:MIN_DP:PL 0/0:39:73:39:0,7 chr9 81166756 . A . . END=81166772 GT:DP:GQ:MIN_DP:PL 0/0:41:99:37:0,111,1362 chr9 81166773 . A . . END=81166773 GT:DP:GQ:MIN_DP:PL 0/0:44:88:44:0,88,1831 chr9 81166774 . C . . END=81167015 GT:DP:GQ:MIN_DP:PL 0/0:49:97:42:0,97,1767 -chr9 81167016 . C T, 66.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=97200.00|79200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=12,15|12,10|0,0;BaseQRankSum=-0.088;DP=49;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=52;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=0.925 GT:AD:DP:GQ:PL:SB 0/1:27,22,0:49:40:74,0,40,924,1134,964:12,15,12,10 +chr9 81167016 . C T, 66.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=97200.00|79200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=12,15|12,10|0,0;BaseQRankSum=-0.088;DP=49;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=53;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=176400,49;ReadPosRankSum=0.925 GT:AD:DP:GQ:PL:SB 0/1:27,22,0:49:40:74,0,40,924,1134,964:12,15,12,10 chr9 81167017 . T . . END=81167106 GT:DP:GQ:MIN_DP:PL 0/0:50:99:47:0,103,1800 chr9 81167107 . A . . END=81167107 GT:DP:GQ:MIN_DP:PL 0/0:44:89:44:0,89,1205 chr9 81167108 . A . . END=81167206 GT:DP:GQ:MIN_DP:PL 0/0:46:92:40:0,92,1648 @@ -5258,9 +5256,9 @@ chr9 81167873 . T . . END=81167873 GT:DP:GQ:MIN_DP:PL 0/0:53:78:53:0,7 chr9 81167874 . C . . END=81167905 GT:DP:GQ:MIN_DP:PL 0/0:52:90:51:0,90,1800 chr9 81167906 . T . . END=81167906 GT:DP:GQ:MIN_DP:PL 0/0:53:80:53:0,80,2194 chr9 81167907 . G . . END=81167929 GT:DP:GQ:MIN_DP:PL 0/0:54:99:51:0,112,1800 -chr9 81167930 . A C, 63.64 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=111600.00|56569.00|0.00;AS_RAW_MQRankSum=|-6.7,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=17,14|9,12|0,0;BaseQRankSum=1.603;DP=52;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=1,0;HAPDOM=0.952,0.00;HEC=40,22;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.633;RAW_MQandDP=168169,52;ReadPosRankSum=0.718 GT:AD:DP:GQ:PL:SB 0/1:31,21,0:52:40:71,0,40,882,1284,922:17,14,9,12 +chr9 81167930 . A C, 63.64 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=111600.00|56569.00|0.00;AS_RAW_MQRankSum=|-6.7,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=17,14|9,12|0,0;BaseQRankSum=1.603;DP=52;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=1,0;HAPDOM=0.952,0.00;HEC=42,22;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.633;RAW_MQandDP=168169,52;ReadPosRankSum=0.718 GT:AD:DP:GQ:PL:SB 0/1:31,21,0:52:40:71,0,40,882,1284,922:17,14,9,12 chr9 81167931 . C . . END=81167961 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,120,1800 -chr9 81167962 . A G, 63.64 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=111364.00|60169.00|0.00;AS_RAW_MQRankSum=|-6.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=19,12|9,13|0,0;BaseQRankSum=0.261;DP=54;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=1,0;HAPDOM=0.909,0.00;HEC=41,21;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.343;RAW_MQandDP=175133,54;ReadPosRankSum=-1.372 GT:AD:DP:GQ:PL:SB 0/1:31,22,0:53:40:71,0,40,924,1302,964:19,12,9,13 +chr9 81167962 . A G, 63.64 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=111364.00|60169.00|0.00;AS_RAW_MQRankSum=|-6.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=19,12|9,13|0,0;BaseQRankSum=0.261;DP=54;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=1,0;HAPDOM=0.909,0.00;HEC=43,21;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.343;RAW_MQandDP=175133,54;ReadPosRankSum=-1.372 GT:AD:DP:GQ:PL:SB 0/1:31,22,0:53:40:71,0,40,924,1302,964:19,12,9,13 chr9 81167963 . G . . END=81168069 GT:DP:GQ:MIN_DP:PL 0/0:57:99:52:0,120,1800 chr9 81168070 . T . . END=81168070 GT:DP:GQ:MIN_DP:PL 0/0:56:70:56:0,70,2275 chr9 81168071 . C . . END=81168253 GT:DP:GQ:MIN_DP:PL 0/0:53:99:49:0,99,1800 @@ -5447,7 +5445,7 @@ chr9 81169540 . G . . END=81169542 GT:DP:GQ:MIN_DP:PL 0/0:19:51:19:0,5 chr9 81169543 . C . . END=81169543 GT:DP:GQ:MIN_DP:PL 0/0:18:36:18:0,36,657 chr9 81169544 . T . . END=81169545 GT:DP:GQ:MIN_DP:PL 0/0:18:16:17:0,16,682 chr9 81169546 . C . . END=81169547 GT:DP:GQ:MIN_DP:PL 0/0:17:51:17:0,51,707 -chr9 81169548 . A ATG, 70.78 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,0|0,0;DP=8;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=37;MLEAC=1,0;MLEAF=0.500,0.00;RAW_MQandDP=28800,8 GT:AD:DP:GQ:PL:SB 1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,3,0 +chr9 81169548 . A ATG, 70.78 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,0|0,0;DP=8;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=38;MLEAC=1,0;MLEAF=0.500,0.00;RAW_MQandDP=28800,8 GT:AD:DP:GQ:PL:SB 1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,3,0 chr9 81169549 . T . . END=81169553 GT:DP:GQ:MIN_DP:PL 0/0:20:12:20:0,12,180 chr9 81169554 . G . . END=81169554 GT:DP:GQ:MIN_DP:PL 0/0:24:27:24:0,27,405 chr9 81169555 . T . . END=81169579 GT:DP:GQ:MIN_DP:PL 0/0:24:33:23:0,33,495 @@ -5895,7 +5893,7 @@ chr9 81173332 . T . . END=81173332 GT:DP:GQ:MIN_DP:PL 0/0:27:62:27:0,6 chr9 81173333 . C . . END=81173338 GT:DP:GQ:MIN_DP:PL 0/0:27:75:26:0,75,1125 chr9 81173339 . A . . END=81173339 GT:DP:GQ:MIN_DP:PL 0/0:27:36:27:0,36,1094 chr9 81173340 . T . . END=81173368 GT:DP:GQ:MIN_DP:PL 0/0:29:81:27:0,81,1209 -chr9 81173369 . A G, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=46800.00|54000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=3,10|6,9|0,0;BaseQRankSum=-0.472;DP=28;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=29;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=100800,28;ReadPosRankSum=0.645 GT:AD:DP:GQ:PL:SB 0/1:13,15,0:28:40:75,0,40,623,546,621:3,10,6,9 +chr9 81173369 . A G, 67.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=50400.00|54000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=3,11|6,9|0,0;BaseQRankSum=-0.537;DP=29;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=30;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.939 GT:AD:DP:GQ:PL:SB 0/1:14,15,0:29:40:75,0,40,623,588,663:3,11,6,9 chr9 81173370 . G . . END=81173384 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1190 chr9 81173385 . C . . END=81173389 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 chr9 81173390 . A . . END=81173396 GT:DP:GQ:MIN_DP:PL 0/0:28:81:27:0,81,1124 @@ -6042,7 +6040,7 @@ chr9 81174437 . T . . END=81174437 GT:DP:GQ:MIN_DP:PL 0/0:38:80:38:0,8 chr9 81174438 . G . . END=81174446 GT:DP:GQ:MIN_DP:PL 0/0:38:99:38:0,105,1575 chr9 81174447 . G . . END=81174447 GT:DP:GQ:MIN_DP:PL 0/0:37:77:37:0,77,1577 chr9 81174448 . C . . END=81174477 GT:DP:GQ:MIN_DP:PL 0/0:34:96:32:0,96,1216 -chr9 81174478 . A C, 157.06 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|115200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|14,18|0,0;DP=32;ExcessHet=0.0000;FILTERED_HAPS=2;HAPCOMP=0,0;HAPDOM=0.594,0.00;HEC=45,13;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=115200,32;XC=1 GT:AD:DP:GQ:PL:SB 1/1:0,32,0:32:96:171,96,0,1440,96,171:0,0,14,18 +chr9 81174478 . A C, 157.06 . ASSEMBLED_HAPS=4;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|115200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|14,18|0,0;DP=32;ExcessHet=0.0000;FILTERED_HAPS=2;HAPCOMP=0,0;HAPDOM=0.594,0.00;HEC=46,13;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=115200,32;XC=1 GT:AD:DP:GQ:PL:SB 1/1:0,32,0:32:96:171,96,0,1440,96,171:0,0,14,18 chr9 81174479 . G . . END=81174479 GT:DP:GQ:MIN_DP:PL 0/0:30:89:30:0,89,760 chr9 81174480 . G . . END=81174480 GT:DP:GQ:MIN_DP:PL 0/0:32:96:32:0,96,1398 chr9 81174481 . G . . END=81174481 GT:DP:GQ:MIN_DP:PL 0/0:30:88:30:0,88,732 @@ -6123,7 +6121,7 @@ chr9 81174895 . T . . END=81174895 GT:DP:GQ:MIN_DP:PL 0/0:33:87:33:0,8 chr9 81174896 . T . . END=81175008 GT:DP:GQ:MIN_DP:PL 0/0:40:91:33:0,91,1164 chr9 81175009 . C . . END=81175009 GT:DP:GQ:MIN_DP:PL 0/0:44:87:44:0,87,1748 chr9 81175010 . T . . END=81175020 GT:DP:GQ:MIN_DP:PL 0/0:44:99:44:0,120,1800 -chr9 81175021 . T A, 64.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|2.0,1|NaN;AS_RAW_MQ=93600.00|68400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=15,11|14,5|0,0;BaseQRankSum=2.089;DP=46;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=46;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=165600,46;ReadPosRankSum=1.965 GT:AD:DP:GQ:PL:SB 0/1:26,19,0:45:40:72,0,40,798,1066,838:15,11,14,5 +chr9 81175021 . T A, 64.64 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=|2.0,1|NaN;AS_RAW_MQ=93600.00|68400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=15,11|14,5|0,0;BaseQRankSum=2.089;DP=46;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=47;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=165600,46;ReadPosRankSum=1.965 GT:AD:DP:GQ:PL:SB 0/1:26,19,0:45:40:72,0,40,798,1066,838:15,11,14,5 chr9 81175022 . A . . END=81175193 GT:DP:GQ:MIN_DP:PL 0/0:44:93:40:0,93,1774 chr9 81175194 . T . . END=81175194 GT:DP:GQ:MIN_DP:PL 0/0:41:18:41:0,18,1268 chr9 81175195 . T . . END=81175208 GT:DP:GQ:MIN_DP:PL 0/0:44:99:40:0,120,1434 @@ -6290,7 +6288,7 @@ chr9 81176496 . C . . END=81176500 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,3 chr9 81176501 . T . . END=81176524 GT:DP:GQ:MIN_DP:PL 0/0:9:21:8:0,21,303 chr9 81176525 . A . . END=81176525 GT:DP:GQ:MIN_DP:PL 0/0:9:0:9:0,0,323 chr9 81176526 . T . . END=81176532 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,295 -chr9 81176533 . T A, 82.02 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|25200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,4|0,0;DP=7;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=9;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=25200,7 GT:AD:DP:GQ:PL:SB 1/1:0,7,0:7:21:96,21,0,315,21,96:0,0,3,4 +chr9 81176533 . T A, 82.02 . ASSEMBLED_HAPS=2;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|25200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,4|0,0;DP=7;ExcessHet=0.0000;FILTERED_HAPS=0;HAPCOMP=0,0;HAPDOM=1.00,0.00;HEC=10;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=25200,7 GT:AD:DP:GQ:PL:SB 1/1:0,7,0:7:21:96,21,0,315,21,96:0,0,3,4 chr9 81176534 . A . . END=81176539 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,325 chr9 81176540 . A . . END=81176541 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,413 chr9 81176542 . T . . END=81176550 GT:DP:GQ:MIN_DP:PL 0/0:10:27:10:0,27,405 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf.idx index ca9a7a40a29..d9dbf915d6c 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf index b783c067b27..c03af82b594 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf @@ -23,7 +23,7 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##contig= ##contig= ##contig= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf.idx index a110b962bac..503b6872771 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/test_flowBasedHMM.expected.vcf.idx differ