I was wondering if someone can help me interpret the --check-sex results I am getting in plink.
When running this command (./plink --bfile file --check-sex 0.35 0.65 ycount out X) , I seem to get a lot of Problems being detected. I have done this a couple of times and ended up focusing on common snps only as I guess rarer snps can cause problems with F! Ran ycount at the same time (although I am only left with 5 SNPs on the Y chromosome) .
PLINK is detecting 58/162 problems in this relatively small cohort!!! The data came from an Affymetrix chip, and the axiom analysis suite is predicting the gender concordant with the pedigree data provided in all of these!
Here are some of the examples
Any idea why this is happening?