I am trying to conduct a GxE in PLINK using a covariate file but PLINK doesn't seem to be recognizing the file. Can someone tell me what I'm doing wrong?
plink --bfile omni --gxe --covar omni.txt
The covariate file omni.txt has the same # of observations as the .fam file and contains FID, IID, Covar1 coded like so...
FID IID Covar1
## ## 1, 2, or -9
The log says that it reads the .bim and .fam files but doesn't even mention the covariate file.