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.
I am trying to set filtered genotypes to no-call:
java -Xmx6g -jar GenomeAnalysisTK.jar
I'm getting this error MESSAGE: Argument with name 'setFilteredGtToNocall' isn't defined.
I can't find anything about this argument elsewhere in the gatk documentation or elsewhere online to point me int he right direction for its usage. Does it work?