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 run MuTect-1.1.7 in standard mode
I run MuTect-1.1.7 for paired tumor-normal exome data. My question is how to run it in standard mode? Is it right to run MuTect by default, and filter the lines in output file with at least one of these four failure reasons (germline_risk, normal_lod, possible_contamination, triallelic_sites) in the second to last field? Thanks very much for your time!