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.
Applying GATK to microbiome data
Hi, I am interested in knowing how to apply gatk tools to microbiome data. Specifically, I would like to override the assumption of ploidy in the HaplotypeCaller and making it flexible, in that one sample could have a unknown number of haplotypes at the same time, I know somatic mutation caller Mutect2 does not share the assumption but then it's designed to specifically deal with normal - tumor sample pair which is not really applicable in the microbiome studies. Thanks