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@meganshand
meganshand committed Aug 6, 2024
1 parent 9f0310c commit 6618ca5
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Showing 3 changed files with 5 additions and 2 deletions.
4 changes: 3 additions & 1 deletion ...rg/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparatorIntegrationTest.java
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Expand Up @@ -24,7 +24,9 @@ public Object[][] getTestVcfs() {
{ " -L chr1:186475", "expected_warning_as_vqslod.txt" },
{ " -L chr1:186475 --ignore-attribute AS_VQSLOD", "empty_file.txt" },
{ " -L chr1:187471 --ignore-attribute AS_VQSLOD", "expected_warning_filter.txt" },
{ " -L chr1:186475-945670 " + DEFAULT_WARP_SETTINGS, "empty_file.txt" },
{ " -L chr1:186475-945669 " + DEFAULT_WARP_SETTINGS, "empty_file.txt" },
{ " -L chr1:945670 " + DEFAULT_WARP_SETTINGS, "qual_diff_warning.txt"}, // different QUAL values
{ " -L chr1:945670 --qual-change-allowed 0.1 --ignore-attribute AS_VQSLOD", "empty_file.txt"},
{ " -L chr1:186475 --mute-acceptable-diffs", "empty_file.txt" } // low quality site is muted even though the AS_VQSLOD is different
};
}
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2 changes: 1 addition & 1 deletion src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf
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Expand Up @@ -3465,4 +3465,4 @@ chr1 944795 . C T 296.62 PASS AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-1.800;AS
chr1 945010 rs3748593 C A 531.62 PASS AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=1.800;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=10.64;AS_ReadPosRankSum=-0.700;AS_SOR=0.632;AS_VQSLOD=8.4110;AS_culprit=AS_MQ;BaseQRankSum=1.83;DB;DP=2238;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.63;ReadPosRankSum=-6.690e-01;SOR=0.632 GT:AD:DP:GQ:PL 0/0:36,0:36:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:37,0:37:60 0/0:27,0:27:60 0/0:36,0:36:60 0/0:38,0:38:60 0/0:35,0:35:60 0/0:35,0:35:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:30,0:30:60 0/0:39,0:39:60 0/0:32,0:32:60 0/0:31,0:31:60 0/0:32,0:32:60 0/0:29,0:29:60 0/0:37,0:37:60 0/0:31,0:31:60 0/0:33,0:33:60 0/0:33,0:33:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:35,0:35:60 0/0:34,0:34:60 0/0:34,0:34:60 0/0:33,0:33:60 0/0:37,0:37:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:29,0:29:60 0/0:34,0:34:60 0/0:33,0:33:60 0/0:31,0:31:60 0/0:40,0:40:60 0/0:36,0:36:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:33,0:33:60 0/0:31,0:31:60 0/0:34,0:34:60 0/0:34,0:34:60 0/0:34,0:34:60 0/0:66,0:66:60 0/0:37,0:37:60 0/0:31,0:31:60 0/1:29,21:50:99:550,0,746 0/0:32,0:32:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:40,0:40:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:41,0:41:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:31,0:31:60 0/0:27,0:27:60
chr1 945086 rs138652036 T C 479.62 PASS AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.400;AS_FS=5.931;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=9.60;AS_ReadPosRankSum=-2.100;AS_SOR=0.162;AS_VQSLOD=4.0849;AS_culprit=AS_ReadPosRankSum;BaseQRankSum=-3.330e-01;DB;DP=2188;ExcessHet=0.0000;FS=5.931;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=9.59;ReadPosRankSum=-2.087e+00;SOR=0.162 GT:AD:DP:GQ:PL 0/0:36,0:36:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:37,0:37:60 0/0:27,0:27:60 0/0:36,0:36:60 0/0:38,0:38:60 0/0:35,0:35:60 0/0:35,0:35:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:30,0:30:60 0/0:39,0:39:60 0/0:32,0:32:60 0/0:31,0:31:60 0/0:32,0:32:60 0/0:29,0:29:60 0/0:24,0:24:50 0/0:31,0:31:60 0/0:33,0:33:60 0/0:33,0:33:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:35,0:35:60 0/0:34,0:34:60 0/0:34,0:34:60 0/0:33,0:33:60 0/0:37,0:37:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:29,0:29:60 0/0:34,0:34:60 0/0:33,0:33:60 0/0:31,0:31:60 0/0:40,0:40:60 0/0:36,0:36:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:33,0:33:60 0/0:31,0:31:60 0/0:34,0:34:60 0/0:34,0:34:60 0/0:34,0:34:60 0/1:29,21:50:99:498,0,759 0/0:37,0:37:60 0/0:31,0:31:60 0/0:39,0:39:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:41,0:41:60 0/0:35,0:35:60 0/0:33,0:33:60 0/0:36,0:36:60 0/0:31,0:31:60 0/0:27,0:27:60
chr1 945573 rs138129954 G A 2776.29 PASS AC=2;AF=0.015;AN=130;AS_BaseQRankSum=0.150;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0156;AS_MQ=54.63;AS_MQRankSum=-0.550;AS_QD=11.24;AS_ReadPosRankSum=-0.300;AS_SOR=0.730;AS_VQSLOD=2.7778;AS_culprit=AS_MQRankSum;BaseQRankSum=1.39;DB;DP=2431;ExcessHet=0.0338;FS=0.000;InbreedingCoeff=-0.0156;MLEAC=2;MLEAF=0.015;MQ=54.82;MQRankSum=0.333;QD=11.24;ReadPosRankSum=0.030;SOR=0.730 GT:AD:DP:GQ:PL 0/0:36,0:36:60 0/0:33,0:33:60 0/0:39,0:39:60 0/0:30,0:30:60 0/0:29,0:29:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:35,0:35:60 0/0:37,0:37:60 0/0:28,0:28:60 0/0:32,0:32:60 0/1:66,52:118:99:1263,0,1714 0/0:30,0:30:60 0/0:36,0:36:60 0/0:64,0:64:60 0/0:34,0:34:60 0/0:36,0:36:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:30,0:30:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:32,0:32:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:117,0:117:60 0/0:26,0:26:60 0/0:33,0:33:60 0/0:32,0:32:60 0/1:71,58:129:99:1544,0,1802 0/0:34,0:34:60 0/0:37,0:37:60 0/0:33,0:33:60 0/0:34,0:34:60 0/0:33,0:33:60 0/0:66,0:66:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:33,0:33:60 0/0:28,0:28:60 0/0:29,0:29:60 0/0:34,0:34:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:35,0:35:60 0/0:31,0:31:60 0/0:27,0:27:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:28,0:28:60 0/0:31,0:31:60
chr1 945670 rs374558436 C T 1359.62 PASS AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-3.400;AS_FS=0.911;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.47;AS_ReadPosRankSum=0.300;AS_SOR=0.581;AS_VQSLOD=7.7760;AS_culprit=AS_MQ;BaseQRankSum=-3.393e+00;DB;DP=2288;ExcessHet=0.0000;FS=0.911;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=14.46;ReadPosRankSum=0.320;SOR=0.581 GT:AD:DP:GQ:PL 0/0:36,0:36:60 0/0:33,0:33:60 0/0:39,0:39:60 0/0:30,0:30:60 0/0:29,0:29:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:35,0:35:60 0/0:37,0:37:60 0/0:28,0:28:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:30,0:30:60 0/0:36,0:36:60 0/0:64,0:64:60 0/0:34,0:34:60 0/0:36,0:36:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:30,0:30:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:32,0:32:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:117,0:117:60 0/0:26,0:26:60 0/0:33,0:33:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:34,0:34:60 0/0:37,0:37:60 0/0:33,0:33:60 0/0:34,0:34:60 0/0:33,0:33:60 0/1:41,53:94:99:1378,0,1117 0/0:34,0:34:60 0/0:31,0:31:60 0/0:33,0:33:60 0/0:28,0:28:60 0/0:29,0:29:60 0/0:34,0:34:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:35,0:35:60 0/0:31,0:31:60 0/0:27,0:27:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:28,0:28:60 0/0:31,0:31:60
chr1 945670 rs374558436 C T 1359.63 PASS AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-3.400;AS_FS=0.911;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.47;AS_ReadPosRankSum=0.300;AS_SOR=0.581;AS_VQSLOD=7.7760;AS_culprit=AS_MQ;BaseQRankSum=-3.393e+00;DB;DP=2288;ExcessHet=0.0000;FS=0.911;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=14.46;ReadPosRankSum=0.320;SOR=0.581 GT:AD:DP:GQ:PL 0/0:36,0:36:60 0/0:33,0:33:60 0/0:39,0:39:60 0/0:30,0:30:60 0/0:29,0:29:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:35,0:35:60 0/0:37,0:37:60 0/0:28,0:28:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:30,0:30:60 0/0:36,0:36:60 0/0:64,0:64:60 0/0:34,0:34:60 0/0:36,0:36:60 0/0:32,0:32:60 0/0:35,0:35:60 0/0:32,0:32:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:30,0:30:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:28,0:28:60 0/0:34,0:34:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:32,0:32:60 0/0:31,0:31:60 0/0:31,0:31:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:117,0:117:60 0/0:26,0:26:60 0/0:33,0:33:60 0/0:32,0:32:60 0/0:38,0:38:60 0/0:34,0:34:60 0/0:37,0:37:60 0/0:33,0:33:60 0/0:34,0:34:60 0/0:33,0:33:60 0/1:41,53:94:99:1378,0,1117 0/0:34,0:34:60 0/0:31,0:31:60 0/0:33,0:33:60 0/0:28,0:28:60 0/0:29,0:29:60 0/0:34,0:34:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:32,0:32:60 0/0:34,0:34:60 0/0:35,0:35:60 0/0:31,0:31:60 0/0:27,0:27:60 0/0:33,0:33:60 0/0:30,0:30:60 0/0:34,0:34:60 0/0:28,0:28:60 0/0:31,0:31:60
1 change: 1 addition & 0 deletions .../org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/qual_diff_warning.txt
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At position chr1:945670 qual scores differ by 0.010000000000218279, which is more than 0.001

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