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
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.