Ancestry inference cases-controls targeted NGS, small gene set

Question

[nikimourtzi23]

Hi,

I am working on rare-variant association studies and I would like to control for population structure, to ensure that cases and controls have the same ethnic background. The problem is that I have targeted ngs data for the cases meaning small number of variants, I worry that the PCA will not perform well , if I perform all the filtering steps (HWE,MAF>0.05,LD pruning) because I will end up with a small number of variants (< 500)

I was thinking also the admixture analysis. Does anybody have any experience with this type of analysis (how to infer ethnicity from targeted ngs data) or could someone propose a paper ?

Appreciate it