I'm just starting my very first genotyping QC in plink and am trying to identify sex discordant individuals in my cohort.
I tried to run sex-check, and I get a return error message and it doesn't create a .sexcheck document:
594398 variants loaded from .bim file. 509 people (160 males, 349 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked. Before main variant filters, 509 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.997959. 594398 variants and 509 people pass filters and QC. Note: No phenotypes present. Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus.
Does anyone know why this would be?