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Table 2 Summary of a number of software features for three imputation programs.

From: Current software for genotype imputation

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

  1. For more details, see the main text
  2. chr., chromosome.