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.
Question and suggestion re -nct & -num_threads options
I'm trying to implement a workflow with GATK for the first time and I'm getting caught out by the -nct/-num_threads options not being compatible with all walkers, erroring and then killing the process.
Can I suggest that if the flags are not implemented/supported by a walker that the option is ignored. The docs don't clarify which walkers work and which don't so I need to test each one. It would be much easier if simply a warning message were given.
Also, I don't fully understand the difference between -nct/-num_threads. Can someone explain it, please?