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GATK 18.104.22.168, 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.
> ---------------------------- > --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. > ----------------------------