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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.