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.
Typical requirements for StructuralVariationDiscoveryPipelineSpark for local execution?
I have a bunch of human whole genome samples at 30X coverage that I want to perform SV analysis. I am already using some other tools but I wanted to give GATK StructuralVariationDiscoveryPipelineSpark a go for its time. I managed to gather all the necessary resources however my initial execution failed due to java heap space error at stage 7 (Used local and did not play around with any heap space parameters on a 64gb machine ). So I am wondering what would be a typical requirement for this workflow and what do broad testers suggest? I have currently 2 computers vacant one with 128gb memory and another with 64 gb of memory.