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.
Long runtime when skipping markduplicates step?
I am experiencing long runtime of serveral days compared to 24 hours when I skip markduplicate step. There is no obvious error message so it is hard to hack. What can be the reason and possible ways to overcome it?
FYI, I am running Queue in standalone mode, no queue manager in use even though I have a working torque setup.