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.

Base recalibration error with miscoded quality score >70

mavershangmavershang Austin,TxMember
edited October 2014 in Ask the GATK team

Hi, I am using GATK 3.2.2 to do base recalibration, and added --allow_potentially_misencoded_quality_scores. However, the process fails with error "we encounter
ed an extremely high quality score (71) with BAQ correction factor of 4".

It seems --fix_misencoded_quality_scores could help it process without poping error, but I am not sure if that is the correct solution.


Best Answer


Sign In or Register to comment.