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Ploidy parameter in UnifiedGenotyper

apandey1apandey1 Member
edited October 2012 in Ask the GATK team


I just want to know what you mean by "-ploidy" in UnifiedGenotyper.

--sample_ploidy / -ploidy ( int with default value 2 )
Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).

I am working on an inbred (homozygous) strain of mice. I have only one sample. Should I use number 2 here that represents the diploid nature of the genome. I am confused as it says Ploidy (number of chromosomes) per sample.




  • delangeldelangel Broad InstituteMember

    Yes, the -ploidy parameter specified the number of chromosome sets per cell - so in your case it should in theory be 2. Even if you work with inbred strains I'd leave it as two. That way, you'd still be detecting heterozygous sites. A het. site in a haploid or inbred sample may indicate a site where there is a mapping error so it's good to detect these sites and to filter them out, otherwise they might be potentially miscalled as homozygous and you'll have false positives.

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