To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Ploidy parameter in UnifiedGenotyper

apandey1apandey1 Member
edited October 2012 in Ask the GATK team

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

Tagged:

Answers

  • 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.

Sign In or Register to comment.