Estimating the genetic population structure of a cohort typically serves two primary goals in GWAS: 1) to characterize the ancestral diversity of the cohort as a descriptive measure and 2) to provide a quantitative estimate of population structure that can be used in QC and in GWAS association models to reduce the risk of false positives. We focus here on use for description and QC, and later discuss methods for controlling for population structure (see Genome-wide Association).
