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.
Reassign all mapping qualities above a certain value
I'm trying to do variant calling on RNA-seq data aligned with Tophat. I know that I need to use SplitNCigarReads, but I'm having some trouble reassigning mapping qualities. I can successfully reassign MQ of 255 as suggested in the best practices, but am still getting errors for MQ values that are above 60. Is there any way that I can reassign all mapping qualities above a certain value? It seems like there's only tools to do this for one specific MQ and not an entire range.