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Ploidy for variant calling of population samples?

ajdashajdash BelgiumPosts: 2Member

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?

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