For a study I need some kind of "decoy" GWAS-data. For this I created a panel with some genes, the same ones as in the real data. From NCBI I fetch some of their SNPs and create my own artificial .ped and .map file. Furthermore I save for each snp if it lies on the X-Chromosome.
I then go on and randomly create female individuals by giving them heterozygous alleles on their X-Chromosome genes. Males only get homozygous ones.
But when I then run pLink with the
--check-sex argument I get a sexcheck file where there's only zeroes in the
SNPSEX column. So do you know how
--check-sex works that I can then create decoy-individuals that reliably (as much as possible) get detected as a given gender?