Just to be sure, if I use the same .txt file (tab delimited, with correct column headers etc.) as the phenotype file and covariate file, do I use --sex (which is my 5th column header in the txt.) or do I include the ,sex, column in the --covar-name argument, or does this not matter at all?
Edit: I've ran a few GWASs using this setup (both with --sex and with ,sex, amongst --covar-name) and none gave an error, I'm just not sure about the specifics on whether it would matter.
Just to be sure, if I use the same .txt file (tab delimited, with correct column headers etc.) as the phenotype file and covariate file, do I use --sex (which is my 5th column header in the txt.) or do I include the ,sex, column in the --covar-name argument, or does this not matter at all?
Edit: I've ran a few GWASs using this setup (both with --sex and with ,sex, amongst --covar-name) and none gave an error, I'm just not sure about the specifics on whether it would matter.