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.
UnifiedGenotyper pooled:how to set the minimum number of reads supporting an alternate allele
I am using the UnifiedGenotyper for pooled samples and would like to set the minimum count (fraction) of reads supporting an alternate allele in order to distinguish low frequency alleles from sequencing errors. Is there a way to do it? I couldn't find a means to do that or the default threshold in the tool's documentation . Thank you for your support.