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!
A way to come up with "truth set" to use VQSR
Dear GATK Team,
I have a question regarding finding cutoffs for hard filtering. I am working with yeast for which we do not have a good true variation set. I am following the best practices and have done the joint genotyping of my samples. To give some idea, my samples are yeast clones isolated from a population at different time points. I was wondering if I can select a subset of variants which are shared amongst more than 2 samples (and thus, more likely to be correct) to use as my "truth set", and thus, use VQSR pipeline instead. Am I doing something obviously wrong with this approach?