The shared ancestry of chromosomes in a population results in haplotype stretches shared by different individuals. Making use of these shared haplotype stretches, and thereby accounting for the correlation of alleles at nearby markers (linkage disequilibrium, LD), statistical algorithms can make inferences about unobserved alleles. To estimate a missing allele at a specific single nucleotide polymorphism (SNP) on a haplotype, these algorithms compare flanking markers with those from other haplotypes in the sample to find appropriate “template” or reference haplotypes to inform an estimate of the missing allele.
