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how to write custom gatherer for GATK walker in qscript

pankajxyzpankajxyz Posts: 3Member

My qscript for GATK printreads walker takes very long time for gather function( BAM gather function) which uses picard mergesamfiles. How can I write custom gather function in qscript to improve the performance.
1. I want to try mutli-threading for picard mergesamfiles ( which is false by default)
2. I also to try simple concatenation of bam files (scattered bam files are already sorted)

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,653Administrator, GATK Developer admin

    Unfortunately we don't have the resources to provide support for Queue-related development, so you'll have to figure it out on your own, sorry. Good luck!

    Geraldine Van der Auwera, PhD

  • pankajxyzpankajxyz Posts: 3Member

    Thanks Geraldine. I will see what I can do to acheive that.

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