Genotype phasing in populations of closely related individuals

Knowledge of phase has many potential applications for empowering genomic information. For example, phase can facilitate the identification of identical by descent sharing between pairs of individuals, as part of the process of genotype imputation, or to facilitate parent of origin of allele modeling in order to quantify the effect of parental imprinting.Long-range phasing and haplotype library imputation are a fast heuristic phasing method that is particularly suited to application in isolated populations, such as those that prevail in animal and plant breeding programs or human populations in remote locations.This chapter describes the general principle of long-range phasing, the specifics of the long-range phasing, and haplotype imputation algorithm implemented in the software AlphaPhase1.1 (Hickey et al., Genet Sel Evol 43:12, 2011). Examples of how to apply AlphaPhase1.1 to different data sets are described with particular reference to the avoidance of common pitfalls. Finally, some notes describing some of the key terms are given.