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Bug in HaplotypeCaller: Lines meant to STDERR go to STDOUT
I use HaplotypeCaller v. 3.6-0-g89b7209. I want to compress the output before writing it to the disk and use command like this:
gatk -T HaplotypeCaller ... -o /dev/stdout | grep -v -e --- -e WARN | bgzip -s - > output.gvcf.gz
The grep command is needed to get around a bug that sends lines meant to STDERR to STDOUT. This is similar to a bug I reported in v. 3.3: