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How can Mutect2 GATK 4 beta be parallelized?

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Hello,

I am creating PoN for Mutect2 and following an instruction in the comments of Mutect2.java

  • gatk-launch --javaOptions "-Xmx4g" Mutect2 \
  • -R ref_fasta.fa \
  • -I normal1.bam \
  • -tumor normal1_sample_name \
  • --germline_resource af-only-gnomad.vcf.gz \
  • -L intervals.list \
  • -O normal1_for_pon.vcf.gz

This task seems to take highly variable time per sample or interval. I also realized that Mutect2 is not a Spark tool in GATK 4.
Is splitting intervals (and maybe --nativePairHmmThreads) only way to parallelize this task?
I wonder if you have any advice on parallelization in running Mutect2.

Thank you!


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