There are several approaches by which ancestry is considered in GWAS. One is self identified ancestry (SIA)/ethnicity/race. There is some utility in using this information as a starting point for addressing population stratification. When subsetting a sample based on SIA, the number of markers violating Hardy Weinberg Equilibrium (HWE) and measures of genomic inflation are greatly reduced. However, SIA alone is usually insufficient even in apparently homogenous samples.5
