Is it better to use PLINK for controlling population stratification or PCA?

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Bayode O Makanjuola

Hello everyone!

Thank you so much for all your recommendations.

Jinho Shin

Dear Davide,

I am struggling with an GWAS using pooled sample from three populations from different regions.

In crude association, I am thinking that the results without stratification are different from that with stratification. But I don't know the best approach to do the analysis.

How about using --within option instead of PCA. Would you let me know the tips ?

Best regards.