If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
DeNovo pipeline, CalculateGenotypePoster
maybe this post is related to this post
When I'm going to run the DeNovo pipeline with the "--skip-population-priors" Calculate Genotype Posteriors (CGP) option I'have in general few high and low DeNovo variants...
SelectVariants... -sn proband -sn mother -sn father
CalculateGenotypePosteriors -ped --skip-population-priors
VariantFiltration -G-filter 'GQ < 20.0'
VariantAnnotator -ped -A PossibleDeNovo
35 DeNovo (21 HiConfDeNovo, 14 LoConfDeNovo)
But when I'm going to include in the Calculate Genotype Posteriors the "-supporting" option with -ped and without the "--skip-population-priors" option, I have:
395 DeNovo (24 HiConfDeNovo, 371 LoConfDeNovo)
GATK v220.127.116.11, WES data, trios
chr16 14013455 . C T 68.23 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0560;FS=0.000;InbreedingCoeff=0.0814;MQ=60.00;QD=34.11;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0
After CGP (with the "-supporting" option)
chr16 14013455 . C T 68.23 PASS AC=1;AF=0.167;AN=6;DP=2;ExcessHet=0.0560;FS=0.000;InbreedingCoeff=0.0814;MQ=60.00;PG=0,21,47;QD=34.11;SOR=0.693;hiConfDeNovo=WES_12-436bis GT:AD:DP:GQ:PL:PP 0/1:0,2:2:20:59,6,0:32,0,20 0/0:0,0:0:21:0,0,0:0,21,47 0/0:0,0:0:21:0,0,0:0,21,47
Without the -supporting option this variant is excluded...
Any advice if I want to use CGP with higher stringency?