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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



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