The current GATK version is 3.6-0
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parallel running in GATK

blueskypyblueskypy Member Posts: 264 ✭✭

In HC, CombineGVCFs, and GenotypeGVCFs, besides running each chr separately in parallel, can I also break a chr into smaller sections and run each in parallel?




  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,739 admin

    That should be fine for GenotypeGVCFs. Not sure about HC and CombineGVCFs as you may run into edge cases at the section starts and ends.

    Geraldine Van der Auwera, PhD

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