GATK markduplicates / applyBQSR / haplotypecaller tools support unix pipe?

Hi,

I'm new in GATK pipeline. Actually I'm studying GATK best practices concerning the Variant Calling pipeline. I am curious to know if the markduplicates / applyBQSR / haplotypecaller tools:

support the Unix pipe, in order to optimize the processing
use all the fields specified in the SAM format or only needs some specific fields (SAM)

Thanks for the help,

Rocco

gatk unix pipe applybqsr markduplicates

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updated 5.6 years ago by Biostar

• written 5.7 years ago by roccostorace •

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