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.
Benefits of running UnifiedGenotyper on multiple samples at the same time
The best practice guide states to call variants across all samples simultaneously. Besides the ease of working with one multi-sample VCF, what advantages are there to calling the variants at the same time? Does GATK leverage information across all samples when making calls? If so, what assumptions is the UnifiedGenotyper making about the relationship of these samples to each other, and what are the effects on the variant calls?