The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Haplotype caller Speed with Multi-sample variant calling

shalabhsumanshalabhsuman NIHMember Posts: 8

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


  • jpuritzjpuritz Member Posts: 6

    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.

Sign In or Register to comment.