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.

bcbio configuration file (bcbio_system.yaml)

Hello!

I have a question regarding how to tune options for specific software (gatk) in bcbio conf file (bcbio_system.yaml).

I want to define GATK PrintReads java memory parameters Xmx like this:

resources:
gatk-printreads:
    jvm_opts: ["-Xmx7000m"]

However, I am not sure if this is the right way to do it, is "gatk-printreads" the right parameter? Or how do I specifically define java options for PrintReads in config file?

I am running bcbio-nextgen 1.0.5 with GATK 3.8.

Thanks!

Tagged:

Issue · Github
by Sheila

Issue Number
2652
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

Sign In or Register to comment.