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 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!