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!
VQSR / CNN filtering for small (~100) gene panels
I'm trying to perform germline variant calling on a panel with ~100 genes. I was wondering what the bare minimum (in terms of sample size) would be for variant filtering via VQSR. If the sample size is prohibitively high given the size of the gene panel, would it be appropriate to pad the training set with exome data from 1000G or ExAC? In general, is there a minimum number of variants needed to train the model?
Also, is there a timeframe for the official release of GATK CNN, and would something like this be applicable to my gene panel once available?
Thanks for your help!