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.

Is it OK to stack IndelRealigner runs

Hi GATK Team,

My question is related to whether it is OK to run IndelRealigner twice on the same .bam file, first individually, and next with its tumor or normal pair. This seems to be what's recommended in the PPT on the google drive titled "Somatic Variant Discovery"

but I wanted to double-check because I also read that IR modifies the mapping quality of reads that it realigns, which might affect the next IR run. Any insight would be much appreciated. Thanks so much.


Sign In or Register to comment.