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BQSR: How to speed this step up?

mscjuliamscjulia United StatesMember

Hi GATK team members,

I am running a 120G WGS bam file through BaseRecalibrator, and it took me more than a day to even finish chr2. I am writing to learn your advice on speeding this step up. Below are some of my thoughts:

  1. I recall GATK version 3 starts its command line by java -Xmx8g... so that I could assign memory. Now with GATK 4, the command line starts with "gatk", so how should I include memory please?
  2. I understand that in theory I could split the bam by chromosome and do BQSR on each and then recombine. I would like to avoid that if all possible, because I have too many samples to handle and doing this will take too much storage space.
  3. Would love to learn how to do a paralleled computing, and/or distribute tasks onto different threads for this step of GATK.

Thanks a lot.

Helen

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