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!
Tool in GATK to gather BQSR reports
I would like to request a feature from the GATK developers to be included in the toolkit. To parallelize BQSR, it is necessary to merge the GATK BQSR reports. I found the following post from a few years ago stating that the tool to gather BQSR reports would be out shortly: http://gatkforums.broadinstitute.org/gatk/discussion/1919/parallelizing-base-quality-score-recalibration
Could you please add this tool to GATK? Not all folks use Queue, and it seems like this is generally useful when trying to parallelize BQSR on large datasets to make it complete in a reasonable amount of time. Given the main method is only a few lines of code, a GATK developer should be able to get this done very quickly.