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 active regions are identified

Dear GATK team,
I am looking into the code of GATK 4.0 and trying to understand how active regions work and are used. Are active regions only those containing substitutions and/or indels? If a region contains only reads that perfectly map on the reference genome, is this still an active region? Is there any realignment in such region?
I cannot find in the code if/where read perfectly mapping on the reference are filtered out from active regions.
Thank you



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