Ancestry inference cases-controls targeted NGS, small gene set
0
0
Entering edit mode
16 months ago

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

ethnicity pca targeted ngs population structure • 287 views
ADD COMMENT

Login before adding your answer.

Traffic: 1208 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6