Splitting bam files to hg19 intervals provide by gatk

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Shashwat Sahay

• April 09, 2025 10:39

Hi Everyone,

I'm working with large WGS BAM files (~200GB each) and running Mutect2 on an HPC setup. One performance improvement I've already implemented is using the 80-region hg19 interval list from GATK to parallelize variant calling.

However, I'm concerned about I/O bottlenecks due to all 80 parallel jobs reading from the same large BAM file. Would it make sense to split the BAM file into smaller per-interval BAMs, matching the interval list, to reduce I/O contention?

Has anyone tried this in a similar setup, and did it lead to measurable improvements in performance or runtime efficiency?

Thanks!

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  David Benjamin

  • April 16, 2025 17:20

  On all hardware in my experience Mutect2's I/O time is very small compared to CPU time.  I don't think you need to worry about I/O contention.  We parallelize WGS bams 100 ways all the time without issue.

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