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Genetic association analyses are often compromised by missing genotypic data. However several imputation methods are available to overcome this in some way. Below an overview of some of the imputation methods that are published.

Category Source Description Performance experience
Imputation MACH MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. None
Imputation fastPHASE The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data. None
Imputation IMPUTE IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes). None
Imputation PLINK PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. None
Imputation Beagle BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. None