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!
Known Sites for GATK's BQSR for non-human data
I am working on non-human data and want to use GATK's Haplotype caller to call variants. I am using the protocol that is listed here.
So far I have reached the indel realignment stage and want to do base recalibration next. Since I do not have known sites, this page in the GATK forum advises you to do an initial round of SNP calling on original un-recalibrated data.
Has anybody experience doing this? Is this initial calling done with UnifiedGenotyper on the indel realigned BAMs, or since I want to use Haploytype Caller downstream, should I use this module instead?
Thanks for your input!