We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Prevent HaplotypeCaller from writing the whole gvcf to standard out

BenediktBenedikt GermanyMember
edited January 2016 in Ask the GATK team

Hey there,

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

IIEBR

Tagged:

Best Answer

Answers

Sign In or Register to comment.