Group | Feature | BEAGLE | IMPUTE | MACH |
---|---|---|---|---|
Accessibility | Operating system | Java (platform independent) | Linux, Windows, MacOS X, Solaris | Linux, MacOS X |
 | Licence | Free | Free for academic use | Not clear |
 | Source code | Not available | Not available | Availability announced |
 | Documentation | Commendable | Clearly structured | Incomplete |
 | Authors' response | Quick and detailed | Quick | Quick |
 | GUI | No | No | No |
Input | Genotype format | Discrete; custom format | Probabilities; custom format | QTDT (Linkage) |
 | Reference format | Custom format | Custom format; prepared HapMap reference available | HapMap format (custom format) |
 | Conversion utilities | Yes | Yes | No |
Processing | Target of imputation | Chromosomes | Chromosomes or segments | Chromosomes |
 | Memory-saving mode | Yes | No | Yes |
 | Known checking errors | None | Missing probability and input check | Problematic handling of missing reference |
 | Runtime [chr. 6] | 350 minutes | 433 minutes | 2781 minutes |
 | Maximum memory allocation | 2GB | 14 GB [<1 GB with ~ 10 MB segments] | 7GB |
 | Memory-saving mode | Yes | No | Yes |
 | Strand orientation | Check | Check + autoflip | Check + autoflip |
Output | Genotypes | Posterior probability | Posterior probability | Posterior probability; allele dosage |
 | Quality measure for imputation | Allelic R2 | Information measure, average of the maximum posterior probabilities | R2; average of the maximum posterior probabilities |
 | Output file size [chr. 6] | 1476 MB | 533 MB | 938 MB |
Miscellaneous | X chromosome imputation | No | Yes | No |
 | Trio data | Yes | No | No |
 | Multi-allelic markers | Yes | No | No |
 | Accuracy estimation | No | Yes | No |