Abnormal p values in in X chrom GWAS using plink

Question

[jp]

Dear all,

I am new to GWAS and i ran into the following problem when I run plink --assoc on my entire sample. I obtain unnatural p values in chromosomes >22 when i pool man an women, regardless of using sex as covariate or not. Stratifying acording to sex gives normal results and i guess there is a correction applicable in plink but which one.

Anyone have an idea what went wrong ?

Thank you jp