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.
Using Mutect2 on FFPE samples to call germline variants
I've followed the topics on Mutect2 and its way to perform reduction of FFPE artifacts from tumor tissue.
However my task is a little different: I would like to use Mutect2 and its way to remove FFPE artifacts in "normal" tissue, to assess germline variants. It is possible to clean from artifact using Mutect2 and subsequently filter out the possible germline variants? And how can I do it?
Thanks for all the help