Current software for genotype imputation.

Authors:
David Ellinghaus, Stefan Schreiber, Andre Franke, Michael Nothnagel
Year of publication:
2009
Volume:
3
Issue:
4
Issn:
1473-9542
Journal title abbreviated:
Hum. Genomics
Journal title long:
Human genomics
Impact factor:
3.327
Abstract:
Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations.