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Characteristics of six currently used imputation programs
| Feature | IMPUTE | MACH | fastPHASE | BEAGLE | PLINK | SNPMStat |
|---|---|---|---|---|---|---|
| Use phenotype | no | no | no | no | no | yes |
| Requires phased data | yes | no | no | no | no | no |
| Model underlying conditional distribution of haplotypes | population-genetic | population-genetic | cluster-based | cluster-based | multinomial | multinomial |
| Explicitly models population structure | no | no | yes | no | no | no |
| Models admixture | no | no | no | no | no | no |
