MaCH (MArkov Chain Haplotyping) is a Hidden Markov Model (HMM) based haplotyper that reconstructs haplotypes from genotypes of unrelated individuals. Three primary utilities of MaCH are (1) to resolve haplotypes from diploid genotypes; (2) impute missing genotypes; and (3) perform disease mapping analysis.
Input Files: --datfile Marker information file for subjects under study. --pedfile Pedigree file for subjects under study.
Q: Where can I find combined HapMap reference files? A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html
Q: Where can I find HapMap III reference files? A: http://www.sph.umich.edu/csg/yli/mach/download/
Q: Does --mle overwrite fed-in genotypes? A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.