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.
GATK and SGE
A quick question about GATK and SGE clusters. I need to run a set of GATK commands on our cluster but I think this was tied with the usage of Queue (may be I am wrong)
I tried to run it through a job manager I use for all the tools I have but I have a memory issue with GATK commands
Invalid maximum heap size: -Xmx4g -jar Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
Using this memory size on local node works great but not in cluster mode.
My question is : can I run GATK on GE without using scala or Queue ?