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GenotypeGVFs, -ploidy

manolismanolis Member ✭✭
edited January 14 in Ask the GATK team

GATK, human WES


I'm using HaplotypeCaller with the -ploidy option for the sex chromosomes:

Male: chr1-22 = ploidy 2
Male: chrX,Y = ploidy 1

Female: chr1-22,X = ploidy 2

With the MergeVcfs I merge the two male gvcfs to one and then I join my cohort gvcfs (males and females samples) with GenomicsDBImport and at the end I'm going to use GenotypeGVCFs.

I cann't figure out how to calculate the ploidy value to set up with GenotypeGVCFs. What is the meaning of "pool" in my case? My male gvcfs have a mixed ploidy. I have to change strategy? I have 50 male and 55 female samples.

Many thanks

> ----------------------------
> --sample_ploidy / -ploidy
> Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
> Sample ploidy - equivalent to number of chromosome copies per pool. For pooled experiments this should be set to the number of samples in pool multiplied by individual sample ploidy.
> ----------------------------
Post edited by manolis on

Best Answer


  • manolismanolis Member ✭✭
    edited January 15

    Hi @AdelaideR

    I had seen the special note, just I made some confusion reading the comment about "--sample_ploidy / -ploidy".

    Many thanks

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