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Ploidy for variant calling of population samples?

ajdashajdash 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?

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  • ajdashajdash BelgiumMember Posts: 2

    Thanks very much.

  • HasaniHasani 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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    @Hasani, the GATK is not designed to call somatic mutations. Our best variant caller, HaplotypeCaller, is currently not able to consider ploidy different than 2, and it is not suited to consider allele ratios that are dramatically divergent from the expected diploid possibilities. Such capabilities are necessary for somatic mutation analysis.

    Geraldine Van der Auwera, PhD

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