I am running quality control (sex discrepancy) on my binary plink files. I am new to GWAS and PLINK in general so I am not really sure about what to do in the following:
I used the command plink --bfile file_name --check-sex and found one individual with
PEDSEX: 2, SNPSEX: 0, status: PROBLEM, and F: 0.2303. I was following a GWAS/quality control manual i found online, and removed that individual form my binary files using --remove.
I then used --impute-sex and realized I brought back the individual to my dataset, now with
PEDSEX: 0, SNPSEX: 0, status: PROBLEM, and F: 0.2303.
(1) Is the impute-sex step necessary? If all the statuses of the other individuals were 'OK', would --impute-sex do anything to those individuals? (2) Should I proceed to the next QC step right after removing that one individual, and not use --impute-sex at all?
Thank you very much!