Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Qual = 0 sites don't count as polymorphic for GVCF mode #4967

Merged
merged 3 commits into from
Jul 3, 2018
Merged

Qual = 0 sites don't count as polymorphic for GVCF mode #4967

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e7c823b
put the epsilon is isPolymorphic for GVCF mode
davidbenjamin Jun 29, 2018
e7f1e41
updated tests after checking that all changes were at QUAL=0 sites as…
davidbenjamin Jun 29, 2018
dd34dff
edited another test vcf
davidbenjamin Jun 29, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 7 additions & 1 deletion ...ava/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AFCalculationResult.java
View file
Open in desktop
Original file line number Diff line number Diff line change
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;
}

/**
Expand Down
4 changes: 2 additions & 2 deletions ...ONTAMINATED.WITH.HCC1143.NORMALS.15PCT.20.10100000-10150000.gatk3.8-1-1-gdde23f56a6.g.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Expand Down
8 changes: 4 additions & 4 deletions ...stitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
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
20 10082902 . C <NON_REF> . . END=10082903 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440
20 10082904 . C <NON_REF> . . END=10082905 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530
Expand Down
8 changes: 4 additions & 4 deletions ...ces/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
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
20 10082893 . C <NON_REF> . . END=10082901 GT:DP:GQ:MIN_DP:PL 0/0:41:99:38:0,99,1485
20 10082902 . C <NON_REF> . . END=10082903 GT:DP:GQ:MIN_DP:PL 0/0:38:96:38:0,96,1440
20 10082904 . C <NON_REF> . . END=10082905 GT:DP:GQ:MIN_DP:PL 0/0:40:99:39:0,102,1530
Expand Down