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.
About java threads in GATK
Since GATK is based on Java, and java is known for spawning multiple threads for many GATK applications like Haplotypecaller, CombineGVCF, GenotypeGVCF, GenomicsDBimport and so on, there are ways to control such thread spawning when you have limited computing resource. In some GATK forums, we have been advised to use -XX:ConcGCThreads and also -XX:ParallelGCThreads. Since their usage requires in-depth understanding of how java multithreading works, it is difficult for me to understand when to use what. Can someone from the GATK developers team explain which -XX method should be used?