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QD and InbreedingCoefficient inconsistent when different thread number used for GenotypeGVCF

SteveLSteveL BarcelonaMember ✭✭

Hi all,

I have been investigating whether threading has a major impact on the output of GenotypeGVCFs, as obviously the more threads we can use the faster we can go, at least to a certain extent. To this end, I have run GenotypeGVCFs using 1,2,4,8,16 threads (using -nt) on the same set of 100 Chr1 WES input files. I have tested with both versions 3.3-0-g42bfc64 for historic reasons and 3.5. I don't see any mention of these issues in 3.6, so I am presuming they haven't been addressed.

I have found that QD and InbreedingCoefficient are not consistently reported. Below we have two positions extracted from the 5 different thread VCF files produced using GenotypeGVCFs from GATK3.5. I the first example you can see that QD id different in each (range 25.63-32.42), while QUAL and DP, and all sample DPs remain the same. What is also strange is that dividing QUAL by any integer <=14 (the DP) never results in the value shown by QD.

Obviously this is quite an ugly position from the start of my files, but there are many such positions throughout. All values are identical apart from the QD.

Is this a known issue? I couldn't find a recent mention when searching the forums.

I think QD is recommended for use in VQSR, so could this affect the downstream classification of reliable positions?

`` Chr1x100.1thread.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 28590 . T TTGG 419.53 . AC=8;AF=1.00;AN=8;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=8;MLEAF=1.00;MQ=30.00;MQ0=0;QD=32.42;SOR=1.085 GT:AD:DP:GQ:PL ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.: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:.:. ./.:2,0:2:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:. ./.:0,0:0:.:. ./.: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:.:. ./.: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:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:.

Chr1x100.2threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 28590 . T TTGG 419.53 . AC=8;AF=1.00;AN=8;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=8;MLEAF=1.00;MQ=30.00;MQ0=0;QD=30.09;SOR=1.085 GT:AD:DP:GQ:PL ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.: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:.:. ./.:2,0:2:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:. ./.:0,0:0:.:. ./.: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:.:. ./.: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:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:.

Chr1x100.4threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 28590 . T TTGG 419.53 . AC=8;AF=1.00;AN=8;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=8;MLEAF=1.00;MQ=30.00;MQ0=0;QD=30.42;SOR=1.085 GT:AD:DP:GQ:PL ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.: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:.:. ./.:2,0:2:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:. ./.:0,0:0:.:. ./.: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:.:. ./.: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:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:.

Chr1x100.8threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 28590 . T TTGG 419.53 . AC=8;AF=1.00;AN=8;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=8;MLEAF=1.00;MQ=30.00;MQ0=0;QD=25.63;SOR=1.085 GT:AD:DP:GQ:PL ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.: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:.:. ./.:2,0:2:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:. ./.:0,0:0:.:. ./.: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:.:. ./.: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:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:.

Chr1x100.16threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 28590 . T TTGG 419.53 . AC=8;AF=1.00;AN=8;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=8;MLEAF=1.00;MQ=30.00;MQ0=0;QD=27.93;SOR=1.085 GT:AD:DP:GQ:PL ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.: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:.:. ./.:2,0:2:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:. ./.:0,0:0:.:. ./.: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:.:. ./.: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:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,3:3:9:135,9,0 ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. ./.:0,0:0:.:. 1/1:0,2:2:6:90,6,0 ./.: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:.:.``

Here is a similar example for InBreedingCoefficient. Everything is identical again (QD included), with the exception of InbreedingCoeff values. Here we have concordance between 2,4,8 threads, but the single thread value (top) is distinct, and the 16 threads value is missing.

Presumably this is not expected behaviour?

`` Chr1x100.1thread.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 1396238 . G T 8892.16 . AC=7;AF=0.035;AN=200;BaseQRankSum=-8.660e-01;ClippingRankSum=0.130;DP=4101;ExcessHet=0.0058;FS=0.000;InbreedingCoeff=0.5559;LikelihoodRankSum=0.628;MLEAC=7;MLEAF=0.035;MQ=60.00;MQ0=0;MQRankSum=0.635;QD=16.32;ReadPosRankSum=0.680;SOR=0.749 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,99,1485 0/0:35,0:35:99:0,99,1485 0/0:36,0:36:99:0,99,1462 0/0:33,0:33:99:0,99,1140 0/0:35,0:35:99:0,102,1275 0/0:36,0:36:99:0,100,1406 0/0:37,0:37:99:0,105,1298 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1485 0/0:35,0:35:99:0,99,1299 0/0:36,0:36:99:0,102,1370 0/0:36,0:36:99:0,102,1358 0/0:36,0:36:99:0,99,1460 0/0:35,0:35:99:0,101,1099 0/0:41,0:41:99:0,99,1457 0/0:35,0:35:99:0,99,1392 0/0:41,0:41:99:0,101,1190 0/0:40,0:40:99:0,105,1575 0/0:38,0:38:99:0,102,1280 0/0:35,0:35:99:0,99,1460 1/1:1,84:85:99:2474,245,0 0/0:37,0:37:99:0,99,1368 0/0:39,0:39:99:0,99,1485 0/0:35,0:35:99:0,99,1328 0/0:39,0:39:99:0,102,1530 0/0:41,0:41:99:0,111,1665 0/0:35,0:35:99:0,105,1081 0/0:39,0:39:99:0,102,1530 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1040 0/1:74,63:137:99:1584,0,1952 0/0:38,0:38:99:0,99,1260 0/0:44,0:44:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:36,0:36:99:0,99,1311 0/0:38,0:38:99:0,99,1443 0/0:39,0:39:99:0,99,1485 0/0:41,0:41:99:0,117,1755 0/0:39,0:39:99:0,102,1360 0/0:34,0:34:99:0,99,1219 0/0:35,0:35:99:0,99,1175 0/0:45,0:45:99:0,117,1755 0/0:37,0:37:99:0,105,1575 0/0:38,0:38:99:0,99,1223 0/0:35,0:35:99:0,99,1075 0/0:39,0:39:99:0,99,1432 0/0:35,0:35:99:0,99,1208 0/0:39,0:39:99:0,114,1710 0/0:35,0:35:99:0,99,1210 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1145 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1298 0/0:40,0:40:99:0,120,1363 0/0:41,0:41:99:0,99,1485 0/0:41,0:41:99:0,111,1665 0/0:33,0:33:99:0,99,1052 0/0:35,0:35:99:0,102,1193 0/0:35,0:35:99:0,102,1530 0/0:33,0:33:99:0,99,1166 0/0:37,0:37:99:0,99,1485 0/0:35,0:35:99:0,99,1251 0/0:33,0:33:99:0,99,1217 0/0:43,0:43:99:0,102,1677 0/0:35,0:35:99:0,102,1482 0/0:41,0:41:99:0,111,1625 0/1:39,35:74:99:832,0,989 0/0:33,0:33:99:0,99,1115 0/0:35,0:35:99:0,99,1485 0/0:46,0:46:99:0,102,1232 0/0:34,0:34:99:0,99,1286 0/0:33,0:33:99:0,99,1116 0/0:42,0:42:99:0,107,1384 0/0:37,0:37:99:0,99,1122 0/0:44,0:44:99:0,114,1710 0/0:44,0:44:99:0,102,1530 0/0:40,0:40:99:0,102,1530 1/1:0,111:111:99:3186,333,0 0/0:43,0:43:99:0,102,1530 0/0:34,0:34:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:44,0:44:99:0,120,1800 0/0:42,0:42:99:0,111,1548 0/0:34,0:34:99:0,99,1165 0/0:35,0:35:99:0,102,1482 0/0:33,0:33:99:0,99,1078 0/0:36,0:36:99:0,99,1470 0/0:40,0:40:99:0,114,1710 0/0:36,0:36:99:0,99,1399 0/0:40,0:40:99:0,99,1485 0/0:34,0:34:99:0,99,1401 0/0:40,0:40:99:0,108,1420 0/0:42,0:42:99:0,99,1385 0/0:37,0:37:99:0,99,1485 0/0:36,0:36:99:0,105,1575 0/0:34,0:34:99:0,99,1221 0/1:85,53:138:99:953,0,1904 0/0:36,0:36:99:0,100,1180 0/0:40,0:40:99:0,120,1239 0/0:39,0:39:99:0,102,1530

Chr1x100.2threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 1396238 . G T 8892.16 . AC=7;AF=0.035;AN=200;BaseQRankSum=-8.660e-01;ClippingRankSum=0.130;DP=4101;ExcessHet=0.0058;FS=0.000;InbreedingCoeff=-0.4804;LikelihoodRankSum=0.628;MLEAC=7;MLEAF=0.035;MQ=60.00;MQ0=0;MQRankSum=0.635;QD=16.32;ReadPosRankSum=0.680;SOR=0.749 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,99,1485 0/0:35,0:35:99:0,99,1485 0/0:36,0:36:99:0,99,1462 0/0:33,0:33:99:0,99,1140 0/0:35,0:35:99:0,102,1275 0/0:36,0:36:99:0,100,1406 0/0:37,0:37:99:0,105,1298 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1485 0/0:35,0:35:99:0,99,1299 0/0:36,0:36:99:0,102,1370 0/0:36,0:36:99:0,102,1358 0/0:36,0:36:99:0,99,1460 0/0:35,0:35:99:0,101,1099 0/0:41,0:41:99:0,99,1457 0/0:35,0:35:99:0,99,1392 0/0:41,0:41:99:0,101,1190 0/0:40,0:40:99:0,105,1575 0/0:38,0:38:99:0,102,1280 0/0:35,0:35:99:0,99,1460 1/1:1,84:85:99:2474,245,0 0/0:37,0:37:99:0,99,1368 0/0:39,0:39:99:0,99,1485 0/0:35,0:35:99:0,99,1328 0/0:39,0:39:99:0,102,1530 0/0:41,0:41:99:0,111,1665 0/0:35,0:35:99:0,105,1081 0/0:39,0:39:99:0,102,1530 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1040 0/1:74,63:137:99:1584,0,1952 0/0:38,0:38:99:0,99,1260 0/0:44,0:44:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:36,0:36:99:0,99,1311 0/0:38,0:38:99:0,99,1443 0/0:39,0:39:99:0,99,1485 0/0:41,0:41:99:0,117,1755 0/0:39,0:39:99:0,102,1360 0/0:34,0:34:99:0,99,1219 0/0:35,0:35:99:0,99,1175 0/0:45,0:45:99:0,117,1755 0/0:37,0:37:99:0,105,1575 0/0:38,0:38:99:0,99,1223 0/0:35,0:35:99:0,99,1075 0/0:39,0:39:99:0,99,1432 0/0:35,0:35:99:0,99,1208 0/0:39,0:39:99:0,114,1710 0/0:35,0:35:99:0,99,1210 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1145 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1298 0/0:40,0:40:99:0,120,1363 0/0:41,0:41:99:0,99,1485 0/0:41,0:41:99:0,111,1665 0/0:33,0:33:99:0,99,1052 0/0:35,0:35:99:0,102,1193 0/0:35,0:35:99:0,102,1530 0/0:33,0:33:99:0,99,1166 0/0:37,0:37:99:0,99,1485 0/0:35,0:35:99:0,99,1251 0/0:33,0:33:99:0,99,1217 0/0:43,0:43:99:0,102,1677 0/0:35,0:35:99:0,102,1482 0/0:41,0:41:99:0,111,1625 0/1:39,35:74:99:832,0,989 0/0:33,0:33:99:0,99,1115 0/0:35,0:35:99:0,99,1485 0/0:46,0:46:99:0,102,1232 0/0:34,0:34:99:0,99,1286 0/0:33,0:33:99:0,99,1116 0/0:42,0:42:99:0,107,1384 0/0:37,0:37:99:0,99,1122 0/0:44,0:44:99:0,114,1710 0/0:44,0:44:99:0,102,1530 0/0:40,0:40:99:0,102,1530 1/1:0,111:111:99:3186,333,0 0/0:43,0:43:99:0,102,1530 0/0:34,0:34:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:44,0:44:99:0,120,1800 0/0:42,0:42:99:0,111,1548 0/0:34,0:34:99:0,99,1165 0/0:35,0:35:99:0,102,1482 0/0:33,0:33:99:0,99,1078 0/0:36,0:36:99:0,99,1470 0/0:40,0:40:99:0,114,1710 0/0:36,0:36:99:0,99,1399 0/0:40,0:40:99:0,99,1485 0/0:34,0:34:99:0,99,1401 0/0:40,0:40:99:0,108,1420 0/0:42,0:42:99:0,99,1385 0/0:37,0:37:99:0,99,1485 0/0:36,0:36:99:0,105,1575 0/0:34,0:34:99:0,99,1221 0/1:85,53:138:99:953,0,1904 0/0:36,0:36:99:0,100,1180 0/0:40,0:40:99:0,120,1239 0/0:39,0:39:99:0,102,1530

Chr1x100.4threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 1396238 . G T 8892.16 . AC=7;AF=0.035;AN=200;BaseQRankSum=-8.660e-01;ClippingRankSum=0.130;DP=4101;ExcessHet=0.0058;FS=0.000;InbreedingCoeff=0.5559;LikelihoodRankSum=0.628;MLEAC=7;MLEAF=0.035;MQ=60.00;MQ0=0;MQRankSum=0.635;QD=16.32;ReadPosRankSum=0.680;SOR=0.749 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,99,1485 0/0:35,0:35:99:0,99,1485 0/0:36,0:36:99:0,99,1462 0/0:33,0:33:99:0,99,1140 0/0:35,0:35:99:0,102,1275 0/0:36,0:36:99:0,100,1406 0/0:37,0:37:99:0,105,1298 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1485 0/0:35,0:35:99:0,99,1299 0/0:36,0:36:99:0,102,1370 0/0:36,0:36:99:0,102,1358 0/0:36,0:36:99:0,99,1460 0/0:35,0:35:99:0,101,1099 0/0:41,0:41:99:0,99,1457 0/0:35,0:35:99:0,99,1392 0/0:41,0:41:99:0,101,1190 0/0:40,0:40:99:0,105,1575 0/0:38,0:38:99:0,102,1280 0/0:35,0:35:99:0,99,1460 1/1:1,84:85:99:2474,245,0 0/0:37,0:37:99:0,99,1368 0/0:39,0:39:99:0,99,1485 0/0:35,0:35:99:0,99,1328 0/0:39,0:39:99:0,102,1530 0/0:41,0:41:99:0,111,1665 0/0:35,0:35:99:0,105,1081 0/0:39,0:39:99:0,102,1530 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1040 0/1:74,63:137:99:1584,0,1952 0/0:38,0:38:99:0,99,1260 0/0:44,0:44:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:36,0:36:99:0,99,1311 0/0:38,0:38:99:0,99,1443 0/0:39,0:39:99:0,99,1485 0/0:41,0:41:99:0,117,1755 0/0:39,0:39:99:0,102,1360 0/0:34,0:34:99:0,99,1219 0/0:35,0:35:99:0,99,1175 0/0:45,0:45:99:0,117,1755 0/0:37,0:37:99:0,105,1575 0/0:38,0:38:99:0,99,1223 0/0:35,0:35:99:0,99,1075 0/0:39,0:39:99:0,99,1432 0/0:35,0:35:99:0,99,1208 0/0:39,0:39:99:0,114,1710 0/0:35,0:35:99:0,99,1210 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1145 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1298 0/0:40,0:40:99:0,120,1363 0/0:41,0:41:99:0,99,1485 0/0:41,0:41:99:0,111,1665 0/0:33,0:33:99:0,99,1052 0/0:35,0:35:99:0,102,1193 0/0:35,0:35:99:0,102,1530 0/0:33,0:33:99:0,99,1166 0/0:37,0:37:99:0,99,1485 0/0:35,0:35:99:0,99,1251 0/0:33,0:33:99:0,99,1217 0/0:43,0:43:99:0,102,1677 0/0:35,0:35:99:0,102,1482 0/0:41,0:41:99:0,111,1625 0/1:39,35:74:99:832,0,989 0/0:33,0:33:99:0,99,1115 0/0:35,0:35:99:0,99,1485 0/0:46,0:46:99:0,102,1232 0/0:34,0:34:99:0,99,1286 0/0:33,0:33:99:0,99,1116 0/0:42,0:42:99:0,107,1384 0/0:37,0:37:99:0,99,1122 0/0:44,0:44:99:0,114,1710 0/0:44,0:44:99:0,102,1530 0/0:40,0:40:99:0,102,1530 1/1:0,111:111:99:3186,333,0 0/0:43,0:43:99:0,102,1530 0/0:34,0:34:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:44,0:44:99:0,120,1800 0/0:42,0:42:99:0,111,1548 0/0:34,0:34:99:0,99,1165 0/0:35,0:35:99:0,102,1482 0/0:33,0:33:99:0,99,1078 0/0:36,0:36:99:0,99,1470 0/0:40,0:40:99:0,114,1710 0/0:36,0:36:99:0,99,1399 0/0:40,0:40:99:0,99,1485 0/0:34,0:34:99:0,99,1401 0/0:40,0:40:99:0,108,1420 0/0:42,0:42:99:0,99,1385 0/0:37,0:37:99:0,99,1485 0/0:36,0:36:99:0,105,1575 0/0:34,0:34:99:0,99,1221 0/1:85,53:138:99:953,0,1904 0/0:36,0:36:99:0,100,1180 0/0:40,0:40:99:0,120,1239 0/0:39,0:39:99:0,102,1530

Chr1x100.8threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 1396238 . G T 8892.16 . AC=7;AF=0.035;AN=200;BaseQRankSum=-8.660e-01;ClippingRankSum=0.130;DP=4101;ExcessHet=0.0058;FS=0.000;InbreedingCoeff=0.5559;LikelihoodRankSum=0.628;MLEAC=7;MLEAF=0.035;MQ=60.00;MQ0=0;MQRankSum=0.635;QD=16.32;ReadPosRankSum=0.680;SOR=0.749 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,99,1485 0/0:35,0:35:99:0,99,1485 0/0:36,0:36:99:0,99,1462 0/0:33,0:33:99:0,99,1140 0/0:35,0:35:99:0,102,1275 0/0:36,0:36:99:0,100,1406 0/0:37,0:37:99:0,105,1298 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1485 0/0:35,0:35:99:0,99,1299 0/0:36,0:36:99:0,102,1370 0/0:36,0:36:99:0,102,1358 0/0:36,0:36:99:0,99,1460 0/0:35,0:35:99:0,101,1099 0/0:41,0:41:99:0,99,1457 0/0:35,0:35:99:0,99,1392 0/0:41,0:41:99:0,101,1190 0/0:40,0:40:99:0,105,1575 0/0:38,0:38:99:0,102,1280 0/0:35,0:35:99:0,99,1460 1/1:1,84:85:99:2474,245,0 0/0:37,0:37:99:0,99,1368 0/0:39,0:39:99:0,99,1485 0/0:35,0:35:99:0,99,1328 0/0:39,0:39:99:0,102,1530 0/0:41,0:41:99:0,111,1665 0/0:35,0:35:99:0,105,1081 0/0:39,0:39:99:0,102,1530 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1040 0/1:74,63:137:99:1584,0,1952 0/0:38,0:38:99:0,99,1260 0/0:44,0:44:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:36,0:36:99:0,99,1311 0/0:38,0:38:99:0,99,1443 0/0:39,0:39:99:0,99,1485 0/0:41,0:41:99:0,117,1755 0/0:39,0:39:99:0,102,1360 0/0:34,0:34:99:0,99,1219 0/0:35,0:35:99:0,99,1175 0/0:45,0:45:99:0,117,1755 0/0:37,0:37:99:0,105,1575 0/0:38,0:38:99:0,99,1223 0/0:35,0:35:99:0,99,1075 0/0:39,0:39:99:0,99,1432 0/0:35,0:35:99:0,99,1208 0/0:39,0:39:99:0,114,1710 0/0:35,0:35:99:0,99,1210 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1145 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1298 0/0:40,0:40:99:0,120,1363 0/0:41,0:41:99:0,99,1485 0/0:41,0:41:99:0,111,1665 0/0:33,0:33:99:0,99,1052 0/0:35,0:35:99:0,102,1193 0/0:35,0:35:99:0,102,1530 0/0:33,0:33:99:0,99,1166 0/0:37,0:37:99:0,99,1485 0/0:35,0:35:99:0,99,1251 0/0:33,0:33:99:0,99,1217 0/0:43,0:43:99:0,102,1677 0/0:35,0:35:99:0,102,1482 0/0:41,0:41:99:0,111,1625 0/1:39,35:74:99:832,0,989 0/0:33,0:33:99:0,99,1115 0/0:35,0:35:99:0,99,1485 0/0:46,0:46:99:0,102,1232 0/0:34,0:34:99:0,99,1286 0/0:33,0:33:99:0,99,1116 0/0:42,0:42:99:0,107,1384 0/0:37,0:37:99:0,99,1122 0/0:44,0:44:99:0,114,1710 0/0:44,0:44:99:0,102,1530 0/0:40,0:40:99:0,102,1530 1/1:0,111:111:99:3186,333,0 0/0:43,0:43:99:0,102,1530 0/0:34,0:34:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:44,0:44:99:0,120,1800 0/0:42,0:42:99:0,111,1548 0/0:34,0:34:99:0,99,1165 0/0:35,0:35:99:0,102,1482 0/0:33,0:33:99:0,99,1078 0/0:36,0:36:99:0,99,1470 0/0:40,0:40:99:0,114,1710 0/0:36,0:36:99:0,99,1399 0/0:40,0:40:99:0,99,1485 0/0:34,0:34:99:0,99,1401 0/0:40,0:40:99:0,108,1420 0/0:42,0:42:99:0,99,1385 0/0:37,0:37:99:0,99,1485 0/0:36,0:36:99:0,105,1575 0/0:34,0:34:99:0,99,1221 0/1:85,53:138:99:953,0,1904 0/0:36,0:36:99:0,100,1180 0/0:40,0:40:99:0,120,1239 0/0:39,0:39:99:0,102,1530

Chr1x100.16threads.10band.Call30.Emit30.GenotypeGVCF.3.5.vcf:1 1396238 . G T 8892.16 . AC=7;AF=0.035;AN=200;BaseQRankSum=-8.660e-01;ClippingRankSum=0.130;DP=4101;ExcessHet=0.0058;FS=0.000;LikelihoodRankSum=0.628;MLEAC=7;MLEAF=0.035;MQ=60.00;MQ0=0;MQRankSum=0.635;QD=16.32;ReadPosRankSum=0.680;SOR=0.749 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,99,1485 0/0:35,0:35:99:0,99,1485 0/0:36,0:36:99:0,99,1462 0/0:33,0:33:99:0,99,1140 0/0:35,0:35:99:0,102,1275 0/0:36,0:36:99:0,100,1406 0/0:37,0:37:99:0,105,1298 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1485 0/0:35,0:35:99:0,99,1299 0/0:36,0:36:99:0,102,1370 0/0:36,0:36:99:0,102,1358 0/0:36,0:36:99:0,99,1460 0/0:35,0:35:99:0,101,1099 0/0:41,0:41:99:0,99,1457 0/0:35,0:35:99:0,99,1392 0/0:41,0:41:99:0,101,1190 0/0:40,0:40:99:0,105,1575 0/0:38,0:38:99:0,102,1280 0/0:35,0:35:99:0,99,1460 1/1:1,84:85:99:2474,245,0 0/0:37,0:37:99:0,99,1368 0/0:39,0:39:99:0,99,1485 0/0:35,0:35:99:0,99,1328 0/0:39,0:39:99:0,102,1530 0/0:41,0:41:99:0,111,1665 0/0:35,0:35:99:0,105,1081 0/0:39,0:39:99:0,102,1530 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1040 0/1:74,63:137:99:1584,0,1952 0/0:38,0:38:99:0,99,1260 0/0:44,0:44:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:36,0:36:99:0,99,1311 0/0:38,0:38:99:0,99,1443 0/0:39,0:39:99:0,99,1485 0/0:41,0:41:99:0,117,1755 0/0:39,0:39:99:0,102,1360 0/0:34,0:34:99:0,99,1219 0/0:35,0:35:99:0,99,1175 0/0:45,0:45:99:0,117,1755 0/0:37,0:37:99:0,105,1575 0/0:38,0:38:99:0,99,1223 0/0:35,0:35:99:0,99,1075 0/0:39,0:39:99:0,99,1432 0/0:35,0:35:99:0,99,1208 0/0:39,0:39:99:0,114,1710 0/0:35,0:35:99:0,99,1210 0/0:37,0:37:99:0,99,1485 0/0:33,0:33:99:0,99,1145 0/0:38,0:38:99:0,105,1575 0/0:35,0:35:99:0,99,1298 0/0:40,0:40:99:0,120,1363 0/0:41,0:41:99:0,99,1485 0/0:41,0:41:99:0,111,1665 0/0:33,0:33:99:0,99,1052 0/0:35,0:35:99:0,102,1193 0/0:35,0:35:99:0,102,1530 0/0:33,0:33:99:0,99,1166 0/0:37,0:37:99:0,99,1485 0/0:35,0:35:99:0,99,1251 0/0:33,0:33:99:0,99,1217 0/0:43,0:43:99:0,102,1677 0/0:35,0:35:99:0,102,1482 0/0:41,0:41:99:0,111,1625 0/1:39,35:74:99:832,0,989 0/0:33,0:33:99:0,99,1115 0/0:35,0:35:99:0,99,1485 0/0:46,0:46:99:0,102,1232 0/0:34,0:34:99:0,99,1286 0/0:33,0:33:99:0,99,1116 0/0:42,0:42:99:0,107,1384 0/0:37,0:37:99:0,99,1122 0/0:44,0:44:99:0,114,1710 0/0:44,0:44:99:0,102,1530 0/0:40,0:40:99:0,102,1530 1/1:0,111:111:99:3186,333,0 0/0:43,0:43:99:0,102,1530 0/0:34,0:34:99:0,99,1485 0/0:36,0:36:99:0,99,1485 0/0:44,0:44:99:0,120,1800 0/0:42,0:42:99:0,111,1548 0/0:34,0:34:99:0,99,1165 0/0:35,0:35:99:0,102,1482 0/0:33,0:33:99:0,99,1078 0/0:36,0:36:99:0,99,1470 0/0:40,0:40:99:0,114,1710 0/0:36,0:36:99:0,99,1399 0/0:40,0:40:99:0,99,1485 0/0:34,0:34:99:0,99,1401 0/0:40,0:40:99:0,108,1420 0/0:42,0:42:99:0,99,1385 0/0:37,0:37:99:0,99,1485 0/0:36,0:36:99:0,105,1575 0/0:34,0:34:99:0,99,1221 0/1:85,53:138:99:953,0,1904 0/0:36,0:36:99:0,100,1180 0/0:40,0:40:99:0,120,1239 0/0:39,0:39:99:0,102,1530 ``

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ack this is why I hate multithreading. It causes the weirdest issues.

    This is definitely not expected behavior as far as I know. But can you please test 3.6 just to be sure that the behavior is the same? Even though this particular issue has not been reported before (and therefore not addressed expressly) there have coincidentally been a few changes to both annotations' calculations, so we need confirmation that the issue persists before we can examine this further.

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