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.
How to emit only "Keep" or "Covered" calls from MuTect
I'm interested in running muTect in a way that it emits only the Pass/Keep calls and filters out all the "Reject" calls internally.
I spent a lot of time on this forum but couldn't find any definite option or flag for this. I understand that I could simply do
'grep -v "REJECT"'
But I was looking to generate an output file that would be passed to next queue command directly.