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Fixing a bug in allele filtering (#7877)
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* [BIOIN-519] Looks like the alleles that were worse than the reference were not ordered correctly

* Tests updated
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@ilyasoifer @jamesemery
ilyasoifer authored and jamesemery committed Jun 1, 2022
1 parent 0bc15ac commit 1ce04fd
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Showing 17 changed files with 202 additions and 190 deletions.
2 changes: 1 addition & 1 deletion ...n/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFilteringHC.java
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Expand Up @@ -64,7 +64,7 @@ int getAlleleLikelihoodVsInverse(final AlleleLikelihoods<GATKRead, Allele> allel
final int[] asPL = genotypingLikelihoods.sampleLikelihoods(0).getAsPLs();

logger.debug(() -> String.format("GAL:: %s: %d %d %d", allele.toString(), asPL[0], asPL[1], asPL[2]));
return (int)phredScaledConfidence;
return Math.min(asPL[1]-asPL[0], asPL[2]-asPL[0]);
}

}
28 changes: 17 additions & 11 deletions ...oadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebase.expected.flowbased.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@
##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SUSP_NOISY_ADJACENT_TP_VARIANT,Number=0,Type=Flag,Description="Indicates a locus where false positive allele might be affecting a true positive allele">
##INFO=<ID=XC,Number=1,Type=Integer,Description="Indicates collapsing took place">
##INFO=<ID=XC,Number=1,Type=Integer,Description="Indicates longer hmer collapsing took place (this is a flow-based specific tag)">
##contig=<ID=chr1,length=248956422,assembly=38>
##contig=<ID=chr2,length=242193529,assembly=38>
##contig=<ID=chr3,length=198295559,assembly=38>
Expand Down Expand Up @@ -4674,10 +4674,14 @@ chr9 81156951 . T <NON_REF> . . END=81156987 GT:DP:GQ:MIN_DP:PL 0/0:42:99:37:0,1
chr9 81156988 . T <NON_REF> . . END=81156988 GT:DP:GQ:MIN_DP:PL 0/0:41:79:41:0,79,1731
chr9 81156989 . A <NON_REF> . . END=81157067 GT:DP:GQ:MIN_DP:PL 0/0:46:99:40:0,100,1560
chr9 81157068 . C <NON_REF> . . END=81157068 GT:DP:GQ:MIN_DP:PL 0/0:52:66:52:0,66,1938
chr9 81157069 . C <NON_REF> . . END=81157112 GT:DP:GQ:MIN_DP:PL 0/0:51:99:47:0,102,1705
chr9 81157113 . G <NON_REF> . . END=81157113 GT:DP:GQ:MIN_DP:PL 0/0:51:97:51:0,97,1361
chr9 81157114 . G <NON_REF> . . END=81157152 GT:DP:GQ:MIN_DP:PL 0/0:55:99:51:0,120,1800
chr9 81157153 . A <NON_REF> . . END=81157153 GT:DP:GQ:MIN_DP:PL 0/0:55:96:55:0,96,2280
chr9 81157069 . C <NON_REF> . . END=81157092 GT:DP:GQ:MIN_DP:PL 0/0:51:99:45:0,106,1800
chr9 81157093 . G <NON_REF> . . END=81157093 GT:DP:GQ:MIN_DP:PL 0/0:44:87:44:0,87,1547
chr9 81157094 . G <NON_REF> . . END=81157097 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,120,1800
chr9 81157098 . T TG,<NON_REF> 27.60 . ASSEMBLED_HAPS=24;BaseQRankSum=-1.149;DP=48;ExcessHet=0.0000;FILTERED_HAPS=22;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=172800,48;ReadPosRankSum=-0.312 GT:AD:DP:GQ:PL:SB 0/1:33,11,0:44:35:35,0,652,129,678,807:16,17,10,1
chr9 81157099 . G <NON_REF> . . END=81157112 GT:DP:GQ:MIN_DP:PL 0/0:47:99:44:0,115,1466
chr9 81157113 . G <NON_REF> . . END=81157113 GT:DP:GQ:MIN_DP:PL 0/0:44:87:44:0,87,1232
chr9 81157114 . G <NON_REF> . . END=81157152 GT:DP:GQ:MIN_DP:PL 0/0:48:99:44:0,107,1800
chr9 81157153 . A <NON_REF> . . END=81157153 GT:DP:GQ:MIN_DP:PL 0/0:48:75:48:0,75,1990
chr9 81157154 . T <NON_REF> . . END=81157501 GT:DP:GQ:MIN_DP:PL 0/0:64:99:53:0,114,1800
chr9 81157502 . T <NON_REF> . . END=81157502 GT:DP:GQ:MIN_DP:PL 0/0:55:97:55:0,97,2304
chr9 81157503 . G <NON_REF> . . END=81157518 GT:DP:GQ:MIN_DP:PL 0/0:51:99:49:0,103,1800
Expand Down Expand Up @@ -5693,8 +5697,10 @@ chr9 81164856 . G <NON_REF> . . END=81164856 GT:DP:GQ:MIN_DP:PL 0/0:46:94:46:0,9
chr9 81164857 . G <NON_REF> . . END=81164871 GT:DP:GQ:MIN_DP:PL 0/0:47:99:46:0,107,1800
chr9 81164872 . A <NON_REF> . . END=81164872 GT:DP:GQ:MIN_DP:PL 0/0:46:98:46:0,98,1686
chr9 81164873 . A <NON_REF> . . END=81165191 GT:DP:GQ:MIN_DP:PL 0/0:51:99:45:0,100,1800
chr9 81165192 . C <NON_REF> . . END=81165192 GT:DP:GQ:MIN_DP:PL 0/0:48:73:48:0,73,1827
chr9 81165193 . T <NON_REF> . . END=81165233 GT:DP:GQ:MIN_DP:PL 0/0:46:99:43:0,100,1505
chr9 81165192 . C <NON_REF> . . END=81165192 GT:DP:GQ:MIN_DP:PL 0/0:47:70:47:0,70,1783
chr9 81165193 . T <NON_REF> . . END=81165211 GT:DP:GQ:MIN_DP:PL 0/0:45:99:42:0,117,1461
chr9 81165212 . C CAG,<NON_REF> 29.60 . ASSEMBLED_HAPS=24;BaseQRankSum=-0.087;DP=47;ExcessHet=0.0000;FILTERED_HAPS=22;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.509;RAW_MQandDP=166105,47;ReadPosRankSum=-2.369;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:40,4,0:44:37:37,0,1635,158,1647,1805:22,18,4,0
chr9 81165213 . G <NON_REF> . . END=81165233 GT:DP:GQ:MIN_DP:PL 0/0:46:99:44:0,120,1800
chr9 81165234 . T <NON_REF> . . END=81165234 GT:DP:GQ:MIN_DP:PL 0/0:46:59:46:0,59,1774
chr9 81165235 . C <NON_REF> . . END=81165253 GT:DP:GQ:MIN_DP:PL 0/0:46:99:43:0,100,1737
chr9 81165254 . A <NON_REF> . . END=81165254 GT:DP:GQ:MIN_DP:PL 0/0:44:97:44:0,97,1755
Expand Down Expand Up @@ -6601,12 +6607,12 @@ chr9 81171245 . A <NON_REF> . . END=81171245 GT:DP:GQ:MIN_DP:PL 0/0:22:21:22:0,2
chr9 81171246 . A <NON_REF> . . END=81171250 GT:DP:GQ:MIN_DP:PL 0/0:22:60:22:0,60,900
chr9 81171251 . T <NON_REF> . . END=81171251 GT:DP:GQ:MIN_DP:PL 0/0:24:27:24:0,27,957
chr9 81171252 . A <NON_REF> . . END=81171253 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765
chr9 81171254 . T <NON_REF> . . END=81171254 GT:DP:GQ:MIN_DP:PL 0/0:20:45:20:0,45,675
chr9 81171255 . AGTGTGTGTGTGTGT A,<NON_REF> 51.60 . ASSEMBLED_HAPS=12;BaseQRankSum=0.349;DP=24;ExcessHet=0.0000;FILTERED_HAPS=6;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.319;RAW_MQandDP=83956,24;ReadPosRankSum=1.876;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:9,3,0:12:59:59,0,304,85,311,397:6,3,1,2
chr9 81171254 . TA T,<NON_REF> 22.60 . ASSEMBLED_HAPS=12;BaseQRankSum=0.000;DP=20;ExcessHet=0.0000;FILTERED_HAPS=2;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.500;RAW_MQandDP=69556,20;ReadPosRankSum=-1.392;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:18,2,0:20:30:30,0,750,84,756,840:14,4,2,0
chr9 81171255 . AGTGTGTGTGTGTGT A,*,<NON_REF> 48.75 . ASSEMBLED_HAPS=12;BaseQRankSum=0.349;DP=24;ExcessHet=0.0000;FILTERED_HAPS=2;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.502;RAW_MQandDP=83956,24;ReadPosRankSum=0.141;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:8,3,2,0:13:23:59,0,304,23,230,686,110,340,657,759:6,2,3,2
chr9 81171270 . G <NON_REF> . . END=81171275 GT:DP:GQ:MIN_DP:PL 0/0:22:24:19:0,24,360
chr9 81171276 . G <NON_REF> . . END=81171279 GT:DP:GQ:MIN_DP:PL 0/0:16:27:14:0,27,405
chr9 81171280 . G <NON_REF> . . END=81171288 GT:DP:GQ:MIN_DP:PL 0/0:15:33:12:0,33,495
chr9 81171289 . T G,<NON_REF> 108.64 . ASSEMBLED_HAPS=12;BaseQRankSum=0.000;DP=12;ExcessHet=0.0000;FILTERED_HAPS=6;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=43200,12;ReadPosRankSum=-0.493 GT:AD:DP:GQ:PL:SB 0/1:8,4,0:12:99:116,0,208,138,220,358:1,7,1,3
chr9 81171289 . T G,<NON_REF> 108.64 . ASSEMBLED_HAPS=12;BaseQRankSum=0.000;DP=12;ExcessHet=0.0000;FILTERED_HAPS=2;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=43200,12;ReadPosRankSum=-0.493 GT:AD:DP:GQ:PL:SB 0/1:8,4,0:12:99:116,0,208,138,220,358:1,7,1,3
chr9 81171290 . G <NON_REF> . . END=81171290 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,482
chr9 81171291 . G <NON_REF> . . END=81171291 GT:DP:GQ:MIN_DP:PL 0/0:12:11:12:0,11,420
chr9 81171292 . T <NON_REF> . . END=81171292 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,477
Expand All @@ -6630,7 +6636,7 @@ chr9 81171389 . T <NON_REF> . . END=81171389 GT:DP:GQ:MIN_DP:PL 0/0:19:12:19:0,1
chr9 81171390 . T <NON_REF> . . END=81171398 GT:DP:GQ:MIN_DP:PL 0/0:18:51:17:0,51,761
chr9 81171399 . G <NON_REF> . . END=81171399 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,687
chr9 81171400 . A <NON_REF> . . END=81171415 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,735
chr9 81171416 . C T,<NON_REF> 343.64 . ASSEMBLED_HAPS=12;BaseQRankSum=0.000;DP=19;ExcessHet=0.0000;FILTERED_HAPS=6;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=68400,19;ReadPosRankSum=-0.821 GT:AD:DP:GQ:PL:SB 0/1:9,9,0:18:99:351,0,351,378,378,756:4,5,2,7
chr9 81171416 . C T,<NON_REF> 343.64 . ASSEMBLED_HAPS=12;BaseQRankSum=0.000;DP=19;ExcessHet=0.0000;FILTERED_HAPS=2;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=68400,19;ReadPosRankSum=-0.821 GT:AD:DP:GQ:PL:SB 0/1:9,9,0:18:99:351,0,351,378,378,756:4,5,2,7
chr9 81171417 . T <NON_REF> . . END=81171417 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,806
chr9 81171418 . G <NON_REF> . . END=81171424 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,830
chr9 81171425 . T <NON_REF> . . END=81171460 GT:DP:GQ:MIN_DP:PL 0/0:22:60:20:0,60,862
Expand Down
Binary file modified ...nstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebase.expected.flowbased.vcf.idx
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