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!