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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
TCGA WGS PoN for CNV
I would like to use a whole genome sequencing TCGA panel of normals for the GATK CNV workflow. I have dbGaP access and can use the controlled access TCGA workspaces. So I was wondering if of such a PoN exist somewhere already or if this is something I have to create with the CNV_Somatic_Panel workflow. I think there are about 1000 WGS normals I could use from the controlled access TCGA workspaces. If I use the CNV_Somatic_Panel workflow do I have to go up on memory in the configuration to process that many samples? What would be good parameters?