Table 2.
Summary of a number of software features for three imputation programs.
| 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 |
For more details, see the main text
chr., chromosome.