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Any way to combine QUAL accross different files when using combine variants?
dg11
Member ✭
Hi. I have a question regarding the QUAL annotation when using combine variants. Essentially, we're calling variants in 4 different African populations with the view to generating and imputation reference panel. In order to preserve the diversity of variants local to each population, we have called variants in these 4 populations separately with unified genotyper (rather than multi-sample calling accross all 4 populations), and have then called same as reference sites accross the union of all sites, to generate a complete squared set. We have then merged these using combinevariants, and run variant annotator to generate annotations accross all individuals in the 4 populations for the VQSR step. However, we run into problems with the QD annotation, which doesn't seem to work in the model, because it seems that QUAL is inherited from the first file in combine variants. Is there any way to get around this issue, and generate QD which is meaningful accross all samples?
I would really appreciate your thoughts on this- please let me know if this is unclear.
Thanks.
Deepti
Answers
Geraldine writes:
http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk
"In the method article Using the Unified Genotyper, there is a link to a document that explains the math of the EXACT model, i.e. how the QUAL value is calulated."
The link to the document describing the QUAL calculation is however dead. Maybe you can provide a new link in this thread? It seems to be a popular question on the internet. Thanks.
I also have a follow-up question. Why does QUAL change between UnifiedGenotyper outputs using -gt_mode DISCOVERY MODE / -out_mode EMIT_VARIANTS_ONLY and -gt_mode GENOTYPE_GIVEN_ALLELES / -out_mode EMIT_ALL_SITES, respectively? Is it dependent on a random seed generator?
-gt_mode DISCOVERY MODE
-out_mode EMIT_VARIANTS_ONLY
1 100008719 . C T 16.99 . AC=7;AF=0.060;AN=116;BaseQRankSum=-5.489;DP=131;Dels=0.00;FS=49.935;HaplotypeScore=0.9374;InbreedingCoeff=-0.1132;MLEAC=8;MLEAF=0.069;MQ=54.05;MQ0=0;MQRankSum=-3.323;QD=1.13;ReadPosRankSum=-1.198;SB=17.80 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6:0,6,74 0/0:2,0:2:6:0,6,77 ./. 0/0:1,0:1:3:0,3,33 0/1:1,1:2:19:19,0,20 ./. ./. ./. ./. 0/0:3,1:4:6:0,6,79 ./. ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:23:23,0,64 ./. 0/0:5,0:5:15:0,15,185 0/0:1,0:1:3:0,3,39 0/0:2,1:3:6:0,6,79 0/0:2,0:2:6:0,6,71 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,69 0/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,39 ./. 0/0:1,0:1:3:0,3,40 ./. 0/0:2,0:2:6:0,6,78 0/0:3,2:5:6:0,6,60 ./../. ./. 0/0:3,0:3:9:0,9,114 ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:20:20,0,60 0/0:3,0:3:9:0,9,98 ./. 0/0:1,0:1:3:0,3,390/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,33 ./. ./.0/0:4,0:4:12:0,12,142 ./. ./. 1/1:0,2:3:3:23,3,0 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3:0,3,33 ./. 0/0:1,0:1:3:0,3,32 0/0:1,0:1:3:0,3,22 ./. ./. 0/0:2,1:3:6:0,6,68 0/0:2,0:2:6:0,6,59 ./. ./. 0/0:4,0:5:12:0,12,155 ./. 0/0:2,1:3:3:0,3,38./. ./. 0/0:1,0:1:3:0,3,38 0/0:1,0:1:3:0,3,38 ./. 0/0:3,1:4:9:0,9,118 ./. ./. 0/0:2,0:2:6:0,6,79 0/1:1,1:2:20:20,0,33 0/1:1,1:2:17:17,0,32 0/0:2,0:2:6:0,6,76 0/0:3,0:3:9:0,9,118 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3:0,3,36 0/0:2,0:2:6:0,6,72 ./. 0/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,30 0/0:3,0:3:9:0,9,117 0/0:1,1:2:3:0,3,39 0/0:2,0:2:6:0,6,59./. 0/0:1,0:1:3:0,3,37 0/0:1,0:1:3:0,3,38 ./. 0/0:5,0:5:12:0,12,154 ./. ./. 0/0:2,0:2:6:0,6,73
-gt_mode GENOTYPE_GIVEN_ALLELES
-out_mode EMIT_ALL_SITES
1 100008719 . C T 33.63 . AC=7;AF=0.060;AN=116;BaseQRankSum=-5.498;DP=131;Dels=0.00;FS=21.362;HaplotypeScore=0.9374;InbreedingCoeff=-0.1132;MLEAC=8;MLEAF=0.069;MQ=54.05;MQ0=0;MQRankSum=-3.225;QD=2.24;ReadPosRankSum=0.143 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6:0,6,74 0/0:2,0:2:6:0,6,77 ./. 0/0:1,0:1:3:0,3,33 0/1:1,1:2:19:19,0,20 ./. ./. ./. ./. 0/0:3,1:4:6:0,6,79 ./. ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:23:23,0,64 ./. 0/0:5,0:5:15:0,15,185 0/0:1,0:1:3:0,3,39 0/0:2,1:3:6:0,6,79 0/0:2,0:2:6:0,6,71 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,690/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,39 ./. 0/0:1,0:1:3:0,3,40 ./. 0/0:2,0:2:6:0,6,78 0/0:3,2:5:6:0,6,60 ./. ./../. 0/0:3,0:3:9:0,9,114 ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:20:20,0,60 0/0:3,0:3:9:0,9,98 ./. 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,33 ./. ./. 0/0:4,0:4:12:0,12,142 ./. ./. 1/1:0,2:3:3:23,3,0 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3:0,3,33 ./. 0/0:1,0:1:3:0,3,32 0/0:1,0:1:3:0,3,22 ./. ./. 0/0:2,1:3:6:0,6,68 0/0:2,0:2:6:0,6,59 ./. ./. 0/0:4,0:5:12:0,12,156 ./. 0/0:2,1:3:3:0,3,38./. ./. 0/0:1,0:1:3:0,3,38 0/0:1,0:1:3:0,3,38 ./. 0/0:3,1:4:9:0,9,118 ./. ./. 0/0:2,0:2:6:0,6,79 0/1:1,1:2:20:20,0,33 0/1:1,1:2:17:17,0,32 0/0:2,0:2:6:0,6,76 0/0:3,0:3:9:0,9,118 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3:0,3,36 0/0:2,0:2:6:0,6,72 ./. 0/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,30 0/0:3,0:3:9:0,9,117 0/0:1,1:2:3:0,3,39 0/0:2,0:2:6:0,6,59./. 0/0:1,0:1:3:0,3,37 0/0:1,0:1:3:0,3,38 ./. 0/0:5,0:5:12:0,12,154 ./. ./. 0/0:2,0:2:6:0,6,73
adding to what tommy said, CombineVariants will not recalculate the QUAL field, it would need read data to do so. His suggestion of running the UG again on the variants is the right way to think about the problem.