Question: Abnormal p values in in X chrom GWAS using plink
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gravatar for jp
3.1 years ago by
jp0
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 • 862 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by jp0
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