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# Ploidy for variant calling of population samples?

BelgiumMember Posts: 2

I am working on population samples from fungi. I am aware that the Haplotype Caller is specific for diploid genomes and the UnifiedGenotyper is preferred for population samples. According to the best practices, I would what like to know what -ploidy should be specified while calling variants of population samples?

• BelgiumMember Posts: 2

Thanks very much.

• GermanyMember Posts: 30

Hi,

I would like to test GATK with calling mutations in human cancer data (I'm aware of MuTect). I'm not quite sure if 2 is the right value I should set ploidy to...could you please clarify how ploidy's value influences the calling method?

Thanks