Haplotype estimation and genotype imputation
Humans inherit one copy of each chromosome from each parent. These chromosome copies consist of sequences of alleles and are referred to as haplotypes. Modern SNP microarrays only assay genotypes at a subset of all polymorphic sites and do not directly measure haplotypes. This chapter provides an overview of statistical models and computational approaches for inferring haplotypes from genotypes and for imputing (predicting) unmeasured genotypes based on dense reference sets of haplotypes. Haplotypes and imputed genotypes form the basis of many downstream analyses in the study of human disease and population genetics.