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

Maximum size for HaplotypeCaller

eflynn90eflynn90 Washington DCMember Posts: 56

I'm running HaplotypeCaller, and I was wondering what a recommended cohort size was. Would 30 to 40 families (100 to 150 individuals) be too large? Is there a maximum recommended size for number of independent alleles/number of individuals? How does the run time scale with additional individuals?




  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,447 admin



    If you are using the newest workflow, there is no limit to the cohort size because you will be calling variants on individual samples then doing joint genotyping on the cohort.

    In our old workflow, we had a limit to the cohort size because we were calling variants on the entire cohort at once. This took up too much computing time and space.

    You can also refer to Best Practices here:


Sign In or Register to comment.