We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
Z-scores for BaseQRankSum
Hi GATK team,
I plotted all BaseQRankSum scores for all SNP loci, which showed two sharp peaks (one around -5 and the other around 0).
I want to know whether the z-scores given by GATK VariantAnnotator is the normal Z score of a rank sum test, that is z<=-3 probably equals to p<0.001. According to my attached image, most SNP sites with z-scores around -5 have the significant quality difference between ref and alt, which should be considered to be filtered. Did I understand correctly?