WHAP (114) and BEAGLE (11) that typically focus on genotypes for a small number of nearby markers when imputing each missing genotype. Tools in the first category can be further sub-divided into those that compare the potential haplotypes for each individual with all other observed haplotypes (e.g. IMPUTE and MACH) and those that compare potential haplotypes for each individual to a representative set of haplotypes (e.g. fastPHASE). Typically, tools that consider all available markers and all available haplotypes can require substantially more intensive computation but do better at estimating missing genotypes, particularly for rare polymorphisms. Table 1 provides a partial list of recent genomewide association scans that used genotype imputation, together with the method(s) used for imputing missing genotypes in each scan.
