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.
Compare MuTect with VarScan 2 and other mutation callers
We recently compared MuTect with VarScan 2 and other mutation callers using validated data. Our results (at http://genomemedicine.com/content/5/10/91) showed MuTect missed some high-quality SNVs. I posted this paper here in a hope that the developers are aware of the pros and cons of MuTect in comparison with other tools.