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[http://www.sph.umich.edu/csg/yli/mach/ '''MaCH'''] (MArkov Chain Haplotyping), mostly known as a software for genotype imputation, is a Hidden Markov Model (HMM) based haplotyper can that reconstruct haplotypes from genotypes of unrelated individuals. Three primary uses of MaCH are (1) to resolve haplotypes from diploid genotypes; (2) impute missing genotypes; and (3) perform disease mapping analysis.  

'''MaCH''' is a tool for haplotyping, genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li. MaCH was first used to imputed missing genotypes in our FUSION genomewide association study ([http://www.sph.umich.edu/csg/abecasis/publications/17463248.html Scott et al, ''Science'', 2007]) and has since been used in the analysis of many other GWAS.

 

 

* The MaCH download page, with source code, executables and reference haplotype files at http://www.sph.umich.edu/csg/abecasis/MaCH/download/

* The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/

== Input Files  ==

== Input Files  ==