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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
MQ for non-variant positions
I need to filter both my variant and non-variant sites for calculation of window-based genetic diversity.
I am going to use the non-variant blocks in gvcf to filter the non-variant sites for coverage and genotype likelihood. However, I am filtering the variant sites also for MQ. To keep things comparable, I'd like to filter the non-variant sites for MQ as well, however, MQ is not reported in gvcf blocks.
Is there a way to get MQ for non-variant positions in gvcf? Or does MQ counted in the calculation of GQ for non-variant sites?