Several software packages have been developed to impute and test SNPs that were not typed directly, such as BIMBAM [Servin and Stephens, 2007], IMPUTE [Marchini et al., 2007], MaCH [Li et al., 2009, 2010], and Beagle [Browning and Browning, 2009]. Two of these methods (BIMBAM and IMPUTE) assess association between genotype and phenotype with a Bayes Factor. We do not consider the Bayesian approach here, but this is discussed by Guan and Stephens [2008].
