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.
How base-recalibrator deals with genuine biases in base quality?
Base quality may be genuinely associated with some covariates. For instance, average base quality may decrease at the end of the run; or average base quality may be genuinely different between the read groups that come from different runs. Will base quality recalibrator preserve the true quality differences in such cases?