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.
UnifiedGenotyper EMIT_ALL_SITES and probabilities at monomorphic sites
I have used UnifiedGenotyper with the EMIT_ALL_SITES option on selected sites of interest. However, in some cases a genotype is called (see below), but no probability is given. Is it possible to force UG to write those probabilities?
Here is a monomorphic site for which no probabilities are given:
1 100008719 . C .13.19 . AN=76;DP=70;MQ=55.57;MQ0=0 GT:DP ./. ./. 0/0:2 ./. 0/0:1 0/0:2 0/0:2 0/0:1 ./. 0/0:2 0/0:3 0/0:2 ./. 0/0:1 0/0:1 0/0:3 ./. 0/0:2 ./. ./. ./. 0/0:1 0/0:1 0/0:3 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:2 ./. ./. ./. 0/0:3 ./. 0/0:1 0/0:1 0/0:2 ./. ./. ./. 0/0:2 ./. 0/0:1 ./.0/0:1 ./. ./. 0/0:3 ./. 0/0:1 0/0:3 0/0:1 0/0:2 ./. 0/0:1 0/0:3 0/0:3 ./. 0/0:2 ./. ./. 0/0:1 ./.
I think I can solve my problem by using the GENOTYPE_GIVEN_ALLELES option in UG. I'm currently checking it.