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.
coverage depth & SNP-calls
In the following small table you can see the relationship of SNP-calls with coverage_depth (DP) for 34 samples. SNP calls extracted from Haplotype_caller module of GATK. As it can bee seen by increasing DP the number of SNP-calls to be decreased. However, my expectation was in opposite. Is there any explanation? Thanks