Sex in covariate file and .fam file

[junling REN]

Hi,

I am using plink2 to run the logistic regression for X chromosome. The sex information was saved in the .fam file. When I put sex in the covariate file, and run plink2 by plink2 -bfile -covar -covar-name sex,age,pc1… -logistic  cold=+alfreq, +machr2, +beta hide-covar -covar-variance-standardize -out, it shows me the high correlation and the redundant Sex information. When I remove sex from covariate file, the error disappears. My question is: does plink2 automatically apply sex information from .fam file as a covarible even there is no sex in covariate file when run the data of X chromosome?

Thank you in advance.

Junling 

[Chris Chang]

From https://www.cog-genomics.org/plink/2.0/assoc#sex :

"chrX is special in two ways:
- First, sex (as defined in the .fam/.psam input file) is normally included as an additional covariate. If you don't want this, add the 'no-x-sex' modifier. Or you can add the 'sex' modifier to include .fam/.psam sex as a covariate everywhere. Whatever you do, don't include sex from the .fam/.psam file and the --covar file at the same time; otherwise the duplicated column will cause the regression to fail."

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