Ancestry selection with PLINK

[Gloria Benoit]

Hi,

I'm currently running GWAS with PLINK, I'm wondering about the correct way to actually screen for ancestry.

I have seen people select europeans (for instance) using --keep, but a colleague filters the individuals in the phenotype file directly (NA for people outside of the ancestry).

I have found that although the results are very correlated, they are not the same.

Is one of these approaches better than the other?

Thank you!