Hi all, I am currently learning how to perform GWAS quality control, and I have a question on the sex check step. As I understand it, the sex check using plink with the 'ycount' option would report female calls as ambiguous if they have more than 0 non missing Y genotypes.
This is definitely evident from my plink files, where I have female samples showing about half the number of non missing Y genotype as the male samples, and they are being flagged as ambiguous. My question is, why would the female samples have any Y genotypes in the first place, when females only have chromosome X? Where do these Y genotypes come from? Thanks!