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.
Ploidy and "Pooled" for the Haplotype Caller
I was reading the haplotype caller documentation and noticed the "--sample_ploidy/-ploidy" flag. The description reads "Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)."
My question is, what exactly is a pooled experiment? Is it when I have multiple samples? I have separate files for each of my 8 samples and the organism only has one chromosome. So would the number I set be 8*1? Or is this pooled number for multiple samples within a file, and in which case, I would specify 1 instead of 8.