Hi, I have a lot of errors when I do the sex check in plink. I have checked the plink.hh file and all the SNPs are on the X chromosome. I do not have a Y chromosome in my data and I have checked for a pseudoregion using --split-x in Plink 1.9. What is the next step? Is it sensible to use the --set-hh-missing which decreases the sex check errors?

Would really appreciate any help with this! Thanks