AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation (SAHLI) to impute alleles and genotypes. A complete description of the methods is given in Hickey et al. (2011b). AlphaImpute consists of a single program however it calls both AlphaPhase1.1 (Hickey et al., 2011a) and GeneProbForAlphaImpute (Kerr and Kinghorn, 1996). All information on the model of analysis, input files and their layout, is specified in a single parameter file.
Please report bugs or suggestions on how the program / user interface / manual could be improved or made more user friendly to John Hickey.
AlphaImpute is available from:
https://bitbucket.org/hickeyjohnteam/alphaimpute
Material available comprises the compiled programs for 64 bit Linux and Mac OSX machines, together with a User Manual and a suite of worked examples.
AlphaImpute is available to the scientific community free of charge. Users are required, however, to credit its use in any publications. Commercial users should contact John Hickey.
Hickey et al. (2011). Segregation analysis and haplotype library imputation to impute SNP alleles in pedigreed populations. Genetics Selection Evolution, 44:9. doi:10.1186/1297-9686-44-9
While every effort has been made to ensure that AlphaImpute does what it claims to do, there is absolutely no guarantee that the results provided are correct. Use of AlphaImpute is entirely at your own risk!
Your welcome to check out our Gibbs sampler (AlphaBayes) specifically designed for GWAS and Genomic Selection. http://sites.google.com/site/hickeyjohn/alphabayes.
The method implemented in AlphaImpute is described in detail in Hickey et al. (2011).
Warning
AlphaImpute only works for multiple chromosomes if using plink files as input.