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.
Prevent HaplotypeCaller from writing the whole gvcf to standard out
I am using the haplotypecaller on our cluster and the stdout is written to a logfile.
Unfortunately HC is writing the whole gvcf to the standard out although I specified an output file.
This means really huge log files that I can not handle.
Is there a way to prevent this behaviour and only get errors/ warnings from the haplotypecaller?
All the best