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.
VQSR working on large dataset
We have a large cohorts of 30x WGS with more than 3000 samples follwing the Best Practices using GATK 4.0.
To joint calling variants for the cohorts, we combined gVCFs and performed genotyping on each chromosome ( by CombineGVCF and GenotypeGVCF module). After that, variants from each chromosome were merged into a single VCF.
We now need to filter variants by VQSR . However, it required too much memory and time. I read the previous post about "Speeding up VQSR for 2000+ WGS samples". @Geraldine_VdAuwera mentioned that GATK team is working on the problem. I wonder whether is a solution for GATK4 now ?