Ploidy parameter in UnifiedGenotyper
Posted in Ask the GATK team | Last updated on 2012-10-19 17:05:42


Comments (1)

Hi,

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.

Thanks


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