Question: Abnormal p values in in X chrom GWAS using plink
gravatar for jp
3.4 years ago by
jp0 wrote:

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.

Gwas all samples not stratified by sex

Anyone have an idea what went wrong ?

Thank you jp

plink gwas • 901 views
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