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.
QC plot examples
I've attached six plots from some QC analysis of my NGS data, using predominantly GATK. The colours should correspond to the same sample in each plot. The bottom-left plot shows 'error rates' per PCR cycle. Is it worth trying to correct for this in variant recalibration? (Sometimes it feels like trying to correct one black-box with another black-box). In the CallableLoci tool (see plot C), how are the different states determined - specifically for 'Low coverage' is it e.g. <10X or ..