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memory requirements for GATK tools

Hi GATK team,

I have been running the BaseRecalibrator tool on a .bam file that is ~100 gb. My job was killed because the memory for the job exceeded the max memory I allotted (8 gb). I have doubled the memory to 16gb and I hope that resolves the issue.
I was wondering if there are guidelines for memory requirements for the various GATK tools (RealignmentTargetCreator, IndelRealigner, BaseRecalibrator, PrintReads, MuTect) specific for files of different sizes? (I searched the documentation but had trouble finding this information). For example, is it known if the BaseRecalibrator tool requires X amount of memory for a file that is 100 gb? This would help me a lot by saving me time in trouble-shooting the memory settings.

Thanks very much,

Best Answer


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