This imputation-based mapping protocol is a 2-step process. First, unmeasured genotypes are imputed in the GWA data. Then, imputed genotypes are tested for association with phenotypes. Multiple methods exist for imputing genotypes from population genetic data [Browning and Browning, 2007; Greenspan and Geiger, 2004; Li et al., 2006; Marchini et al., 2007; Scheet and Stephens, 2006; Stephens and Scheet, 2005]; for a review see Browning [2008]. Here we focus on the second step, testing the imputed genotypes for association with a trait of interest.
