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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Haplotype caller Speed with Multi-sample variant calling

I am testing out GATK Haplotype caller to make it work with our existing variant calling pipeline. In our current pipeline which is based on GATK best practice, the variants are called globally across the whole population, ie, the VCF file contains genotypes of 1000+ subjects.
From my initial testing with Haplotype caller so far, I have noticed that the caller is too slow (remaining time is 80+ hours and growing…), when I am using it with 1000+ samples and a short exome region interval file, 8 threads and SGE with 16 nodes.
Do you have suggestions on how to speed up the caller; or how to go about multisample variant calling (1000+) with Haplotype caller in the most efficient manner?

P.S. I am using GATK-2.7


Best Answer


  • If there is a logical way to break up your individuals. I seriously recommend the scatter-gather technique, and just try to break things up in 100 individual chunks. Depending on your system, you could run these instances in parallel and save a lot of computation time.

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