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 does MuTect handles overlapping reads?

jorgezajglajorgezajgla MexicoMember

I am aware that haplotype caller corrects for overlapping reads (e.g. fragment size smaller than sum of PE reads), but I could not find information if MuTect provides this or I should merge/clean PE reads before aligning.


Best Answers


Sign In or Register to comment.