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!

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    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.