If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

-nct > 8 makes printreads slower (in apply-bqsr)?

jyjungjyjung Harvard Medical SchoolMember


I am trying to test -nct parameter in printreads (bqsr). My machine has 32 cores (aws cc2.8xlarge) and input is a single BAM. So I tried "-nct 32" first, but it was almost as slow as "-nct 1". Actually any -nct >8 made it slow, so I am wondering if it's my fault or known/expected result. Thanks!

Best Answer


Sign In or Register to comment.