Maximum size for HaplotypeCaller
Posted in Ask the GATK team | Last updated on

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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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