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.
Decreasing heterozygosity parameter increases number of variants called
I am calling variants in exome resequencing of a sample of inbred barley lines using the HaplotypeCaller. Initially, I set the heterozygosity parameter to 0.008, which is the average coding sequence diversity (Tajima's pi) in cultivated barley. In the 60MB capture, I call about 500,000 single nucleotide variants, which seems appropriate given our previous information.
Our collaborators asked us to re-run the variant calling with the default parameters, to see what effect changing the heterozygosity parameter has. When I do, the HaplotypeCaller calls almost one million variants, over twice what we would expect.
Why would this be? Intuitively, I would expect that decreasing the heterozygosity parameter by almost an order of magnitude would under-call variants. Instead, it has the opposite effect.
I am using GATK 2.8-1. Thank you!