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.
HaplotypeCaller on 2000 samples, feasible?
I have previously tested HaplotypeCaller (GATK 2.7) on 100 samples. It takes a long time to run compared to UnifiedGenotyper. Is it feasible to use HaplotypeCaller on 2000 samples? Can I make it run faster other than by using multi-threading? Would it be an advantage for me to run ReduceReads prior to variant calling? I know the details are sparse, but I currently do not have any additional information. Thank you.