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Qual = 0 sites don't count as polymorphic for GVCF mode (#4967)
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@davidbenjamin
davidbenjamin authored Jul 3, 2018
1 parent 6129359 commit ddf042a
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Showing 4 changed files with 17 additions and 11 deletions.
8 changes: 7 additions & 1 deletion ...ava/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AFCalculationResult.java
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Expand Up @@ -21,6 +21,12 @@ public final class AFCalculationResult {
private static final int AF1p = 1;
private static final int LOG_10_ARRAY_SIZES = 2;

// In GVCF mode the STANDARD_CONFIDENCE_FOR_CALLING is 0 by default, and it's nice having this easily-interpretable
// threshold that says "call anything with any evidence at all." The problem is that *everything* has at least some evidence,
// so this would end up putting every site, or at least too many sites, in the gvcf. Thus this parameter is in place to say
// that "0" really means "epsilon."
private static final double EPSILON = 1.0e-10;

private final double[] log10LikelihoodsOfAC;
private final double[] log10PriorsOfAC;
private final double[] log10PosteriorsOfAC;
Expand Down Expand Up @@ -206,7 +212,7 @@ public String toString() {
*/
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
Utils.nonNull(allele);
return getLog10PosteriorOfAFEq0ForAllele(allele) < log10minPNonRef;
return getLog10PosteriorOfAFEq0ForAllele(allele) + EPSILON < log10minPNonRef;
}

/**
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4 changes: 2 additions & 2 deletions ...ONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.g.vcf
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Expand Up @@ -494,7 +494,7 @@
20 10132679 . T <NON_REF> . . END=10132679 GT:DP:GQ:MIN_DP:PL 0/0:63:87:63:0,87,1305
20 10132680 . G <NON_REF> . . END=10132680 GT:DP:GQ:MIN_DP:PL 0/0:64:90:64:0,90,1350
20 10132681 . T <NON_REF> . . END=10132681 GT:DP:GQ:MIN_DP:PL 0/0:63:87:63:0,87,1305
20 10132682 . ATGTGTGTGTGTGTG A,ATGTGTGTGTGTG,<NON_REF> 0 . BaseQRankSum=-1.153;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=0,0,0;MLEAF=0.00,0.00,0.00;MQRankSum=2.033;RAW_MQ=187276.00;ReadPosRankSum=-1.246 GT:AD:DP:GQ:PL:SB 0/0:20,0,3,0:23:81:0,81,1219,85,714,1074,113,1009,938,1152:10,10,0,3
20 10132682 . A <NON_REF> . . END=10132696 GT:DP:GQ:MIN_DP:PL 0/0:63:0:52:0,0,1240
20 10132697 . T <NON_REF> . . END=10132697 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,1312
20 10132698 . G <NON_REF> . . END=10132704 GT:DP:GQ:MIN_DP:PL 0/0:51:60:48:0,60,900
20 10132705 . T <NON_REF> . . END=10132705 GT:DP:GQ:MIN_DP:PL 0/0:50:32:50:0,32,1691
Expand Down Expand Up @@ -591,7 +591,7 @@
20 10140159 . A <NON_REF> . . END=10141258 GT:DP:GQ:MIN_DP:PL 0/0:81:99:41:0,114,1540
20 10141259 . G <NON_REF> . . END=10141259 GT:DP:GQ:MIN_DP:PL 0/0:98:0:98:0,0,2798
20 10141260 . C <NON_REF> . . END=10141439 GT:DP:GQ:MIN_DP:PL 0/0:76:99:67:0,120,1800
20 10141440 . T C,<NON_REF> 0 . BaseQRankSum=-3.862;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-4.968;RAW_MQ=253436.00;ReadPosRankSum=-0.008 GT:AD:DP:GQ:PL:SB 0/0:60,13,0:73:91:0,91,2184,180,2193,2281:30,30,8,5
20 10141440 . T <NON_REF> . . END=10141440 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,1964
20 10141441 . G <NON_REF> . . END=10141691 GT:DP:GQ:MIN_DP:PL 0/0:74:99:59:0,120,1800
20 10141692 . A G,<NON_REF> 0 . BaseQRankSum=-4.974;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=1.855;RAW_MQ=229044.00;ReadPosRankSum=-0.506 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:58,14,0:72:55:0|1:10141692_A_G:0,55,3517,181,3526,3652:35,23,8,6
20 10141693 . A <NON_REF> . . END=10141699 GT:DP:GQ:MIN_DP:PL 0/0:76:99:74:0,120,1800
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8 changes: 4 additions & 4 deletions ...stitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
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Expand Up @@ -227,7 +227,7 @@
20 10004219 . C <NON_REF> . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:52:72:51:0,72,1080
20 10004222 . C CA,<NON_REF> 12.96 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=121951.00|23791.00|0.00;AS_RAW_MQRankSum=|-2.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=18,13|4,4|0,0;BaseQRankSum=0.335;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=198329.00;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
20 10004223 . A AG,<NON_REF> 47.73 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=108277.00|39441.00|0.00;AS_RAW_MQRankSum=|1.8,1|NaN;AS_RAW_ReadPosRankSum=|2.2,1|NaN;AS_SB_TABLE=16,20|5,6|0,0;BaseQRankSum=-0.480;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=214369.00;ReadPosRankSum=2.234 GT:AD:DP:GQ:PL:SB 0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
20 10004224 . A G,<NON_REF> 0 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=152618.00|10800.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=20,28|2,1|0,0;BaseQRankSum=-0.343;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.609;RAW_MQ=227310.00;ReadPosRankSum=1.728 GT:AD:DP:GQ:PL:SB 0/0:48,3,0:51:95:0,95,1492,143,1500,1549:20,28,2,1
20 10004224 . A <NON_REF> . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,450
20 10004225 . A <NON_REF> . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,114,1710
20 10004241 . G <NON_REF> . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965
20 10004242 . A <NON_REF> . . END=10004350 GT:DP:GQ:MIN_DP:PL 0/0:73:99:58:0,120,1800
Expand Down Expand Up @@ -1210,7 +1210,7 @@
20 10074807 . C <NON_REF> . . END=10075042 GT:DP:GQ:MIN_DP:PL 0/0:68:99:56:0,120,1800
20 10075043 . T C,<NON_REF> 2405.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|216841.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,25|0,0;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=220441.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2434,184,0,2434,184,2434:0,0,36,25
20 10075044 . C <NON_REF> . . END=10075141 GT:DP:GQ:MIN_DP:PL 0/0:55:99:51:0,120,1800
20 10075142 . G A,<NON_REF> 0 . AS_RAW_BaseQRankSum=|-2.5,1|NaN;AS_RAW_MQ=211318.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|-2.4,1|NaN;AS_SB_TABLE=36,25|0,4|0,0;BaseQRankSum=-2.480;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.359;RAW_MQ=222959.00;ReadPosRankSum=-2.348 GT:AD:DP:GQ:PL:SB 0/0:61,4,0:65:92:0,92,2165,183,2177,2268:36,25,0,4
20 10075142 . G <NON_REF> . . END=10075142 GT:DP:GQ:MIN_DP:PL 0/0:65:91:65:0,91,2199
20 10075143 . A <NON_REF> . . END=10075167 GT:DP:GQ:MIN_DP:PL 0/0:81:99:68:0,120,1800
20 10075168 . C T,<NON_REF> 3612.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|309981.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,50|0,0;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=309981.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:3641,264,0,3641,264,3641:0,0,38,50
20 10075169 . G <NON_REF> . . END=10075488 GT:DP:GQ:MIN_DP:PL 0/0:67:99:49:0,99,1485
Expand Down Expand Up @@ -1249,9 +1249,9 @@
20 10081751 . T <NON_REF> . . END=10081799 GT:DP:GQ:MIN_DP:PL 0/0:77:99:68:0,120,1800
20 10081800 . C T,<NON_REF> 1109.77 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=126000.00|118800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=26,9|17,16|0,0;BaseQRankSum=0.241;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=-1.082 GT:AD:DP:GQ:PL:SB 0/1:35,33,0:68:99:1138,0,1222,1244,1322,2565:26,9,17,16
20 10081801 . A <NON_REF> . . END=10082884 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,111,1665
20 10082885 . A C,<NON_REF> 0 . AS_RAW_BaseQRankSum=|-2.3,1|NaN;AS_RAW_MQ=147600.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-2.4,1|NaN;AS_SB_TABLE=18,23|0,2|0,0;BaseQRankSum=-2.266;ClippingRankSum=0.000;DP=43;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQ=154800.00;ReadPosRankSum=-2.350 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:41,2,0:43:93:0|1:10082885_A_C:0,93,1525,123,1531,1561:18,23,0,2
20 10082885 . A <NON_REF> . . END=10082885 GT:DP:GQ:MIN_DP:PL 0/0:43:83:43:0,83,1521
20 10082886 . C <NON_REF> . . END=10082891 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,99,1485
20 10082892 . C T,<NON_REF> 1712.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|155641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|20,24|0,0;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=155641.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,44,0:44:99:0|1:10082885_A_C:1741,132,0,1741,132,1741:0,0,20,24
20 10082892 . C T,<NON_REF> 1712.77 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|155641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|20,24|0,0;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=155641.00 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1741,132,0,1741,132,1741:0,0,20,24
20 10082893 . C <NON_REF> . . END=10082901 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1485
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20 10082904 . C <NON_REF> . . END=10082905 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530
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8 changes: 4 additions & 4 deletions ...ces/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
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Expand Up @@ -220,7 +220,7 @@
20 10004219 . C <NON_REF> . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:52:72:51:0,72,1080
20 10004222 . C CA,<NON_REF> 12.96 . BaseQRankSum=0.335;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=198329.00;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
20 10004223 . A AG,<NON_REF> 47.73 . BaseQRankSum=-0.480;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=214369.00;ReadPosRankSum=2.234 GT:AD:DP:GQ:PL:SB 0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
20 10004224 . A G,<NON_REF> 0 . BaseQRankSum=-0.343;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.609;RAW_MQ=227310.00;ReadPosRankSum=1.728 GT:AD:DP:GQ:PL:SB 0/0:48,3,0:51:95:0,95,1492,143,1500,1549:20,28,2,1
20 10004224 . A <NON_REF> . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:70:0:70:0,0,450
20 10004225 . A <NON_REF> . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,114,1710
20 10004241 . G <NON_REF> . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965
20 10004242 . A <NON_REF> . . END=10004350 GT:DP:GQ:MIN_DP:PL 0/0:73:99:58:0,120,1800
Expand Down Expand Up @@ -1203,7 +1203,7 @@
20 10074807 . C <NON_REF> . . END=10075042 GT:DP:GQ:MIN_DP:PL 0/0:68:99:56:0,120,1800
20 10075043 . T C,<NON_REF> 2405.77 . DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=220441.00 GT:AD:DP:GQ:PL:SB 1/1:0,61,0:61:99:2434,184,0,2434,184,2434:0,0,36,25
20 10075044 . C <NON_REF> . . END=10075141 GT:DP:GQ:MIN_DP:PL 0/0:55:99:51:0,120,1800
20 10075142 . G A,<NON_REF> 0 . BaseQRankSum=-2.480;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.359;RAW_MQ=222959.00;ReadPosRankSum=-2.348 GT:AD:DP:GQ:PL:SB 0/0:61,4,0:65:92:0,92,2165,183,2177,2268:36,25,0,4
20 10075142 . G <NON_REF> . . END=10075142 GT:DP:GQ:MIN_DP:PL 0/0:65:91:65:0,91,2199
20 10075143 . A <NON_REF> . . END=10075167 GT:DP:GQ:MIN_DP:PL 0/0:81:99:68:0,120,1800
20 10075168 . C T,<NON_REF> 3612.77 . DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=309981.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:3641,264,0,3641,264,3641:0,0,38,50
20 10075169 . G <NON_REF> . . END=10075488 GT:DP:GQ:MIN_DP:PL 0/0:67:99:49:0,99,1485
Expand Down Expand Up @@ -1242,9 +1242,9 @@
20 10081751 . T <NON_REF> . . END=10081799 GT:DP:GQ:MIN_DP:PL 0/0:77:99:68:0,120,1800
20 10081800 . C T,<NON_REF> 1109.77 . BaseQRankSum=0.241;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=-1.082 GT:AD:DP:GQ:PL:SB 0/1:35,33,0:68:99:1138,0,1222,1244,1322,2565:26,9,17,16
20 10081801 . A <NON_REF> . . END=10082884 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,111,1665
20 10082885 . A C,<NON_REF> 0 . BaseQRankSum=-2.266;ClippingRankSum=0.000;DP=43;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQ=154800.00;ReadPosRankSum=-2.350 GT:AD:DP:GQ:PGT:PID:PL:SB 0/0:41,2,0:43:93:0|1:10082885_A_C:0,93,1525,123,1531,1561:18,23,0,2
20 10082885 . A <NON_REF> . . END=10082885 GT:DP:GQ:MIN_DP:PL 0/0:43:83:43:0,83,1521
20 10082886 . C <NON_REF> . . END=10082891 GT:DP:GQ:MIN_DP:PL 0/0:43:99:42:0,99,1485
20 10082892 . C T,<NON_REF> 1712.77 . DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=155641.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,44,0:44:99:0|1:10082885_A_C:1741,132,0,1741,132,1741:0,0,20,24
20 10082892 . C T,<NON_REF> 1712.77 . DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=155641.00 GT:AD:DP:GQ:PL:SB 1/1:0,44,0:44:99:1741,132,0,1741,132,1741:0,0,20,24
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20 10082904 . C <NON_REF> . . END=10082905 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530
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