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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
getting high quality monomorphic sites from GenotypeGVCFs
I am doing a population genetic analysis and am consequently very interested in obtaining high confidence monomorphic sites.
I used GATK 3.1 HaplotypeCaller in the new incremental variant discovery pipeline and then ran GenotypeGVCFs using the -inv option so as to print non variant sites after combining.
A monomorphic record looks like this:
scaffold_1 202986 . G . . . . GT:AD:DP:PL ./.:81:81:0 ./.:6:12:0 ./.:0:0:0 .....etc
I had a couple of questions:
It seems GT, GQ, and PL is no longer reported after combining for monomorphic sites? is there a reason why? I'm asking because I'd like to be able to distinguish high qual (first genotype) / low qual (second genotype) monomorphic sites so I can change the low qual sites to missing (third genotype).
If getting high confidence monomorphic sites is my goal, would you recommend that I do my own parsing starting with the individual gvcfs rather than using the GenotypeGVCFs walker?
thanks much for your help!
Young Wha Lee