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!
HalplotypeCaller and genotypeGVCFs in joint calling
HC has four major steps: 1) Define active regions. 2) Determine haplotypes by re-assembly of the active region; 3) Determine likelihoods of the haplotypes given the read data; 4) Assign sample genotypes.
In joint calling, which of those steps 1-3 uses the pulled reads from the cohort instead of run within each sample like step 4?
If any of the first three steps uses cohort reads, how is it done if all sample files are in gVCF?