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GATK and PBS clusters

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

has someone some more experience with running GATK on PBS computer clusters ? We have a PBS cluster at UCSF, and the jobs in GATK3.5 calling IR, BQSR, and MUTECT2 stop for some reason (possibly related to memory). Has GATK 3.x and 4.x been tested on PBS clusters, and if so, how does it run ? many thanks,

-- bogdan


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