Plink genomic inflation estimate
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4 months ago
nhaus ▴ 130

I am currently performing a GWAS using a Illumina genotyping chip and PLINK2.

As part of the preprocessing I looked into the population stratification of my cohort and observed that all individuals come from Europe (which is what I also expected). Nonethless, I included the first 10 principal components as covariates in the linear association model. PLINK2 returned a genomic inflation estimate of 1.00085. If I rerun the analysis, but exclude the PC as covariates, I still get a genomic inflation estimate of 1.00159 which is still very close to 1.

So my question is, if I even need to include the PCs as covariates as it seems like there is no population stratification at all.

plink inflation genomic GWAS • 136 views