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.