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.

about mapping quality in GenomeSTRiP

Bazinga199122Bazinga199122 BeijingMember

I am using GenomeSTRiP to call deletions, I want to know how to set the threshold of mapping quality of my reads(for example 20). Can anyone help me with that? Thanks a lot!


  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    To change the mapping quality threshold used in deletion discovery, use "-P select.minimumPairMappingQuality:20".

    There is a different setting to control the mapping quality filter used in genotyping: "-P pairs.minimumMappingQuality:20".

    See also conf/genstrip_parameters.txt.

Sign In or Register to comment.