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Maximum size for HaplotypeCaller

eflynn90eflynn90 Washington DCPosts: 56Member

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?

Thanks,
Elise

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Answers

  • SheilaSheila Broad InstitutePosts: 1,258Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @eflynn90

    Hi,

    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: https://www.broadinstitute.org/gatk/guide/best-practices

    -Sheila

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