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An earlier version of this page is available at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/input_files.html.
MACH input files include information on experimental genotypes for a set of individuals and, optionally, on a set of known haplotypes. MACH can use these to estimate haplotypes for each sampled individual (conditional on the observed genotypes) or to fill in missing genotypes (conditional on observed genotypes at flanking markers and on the observed genotypes at other individuals). Since an essential first step in any analysis is to make sure data is formatted correctly, it is worthwhile to go over the input files MACH expects and their formats.
MACH input files include information on experimental genotypes for a set of individuals and, optionally, on a set of known haplotypes. MACH can use these to estimate haplotypes for each sampled individual (conditional on the observed genotypes) or to fill in missing genotypes (conditional on observed genotypes at flanking markers and on the observed genotypes at other individuals). Since an essential first step in any analysis is to make sure data is formatted correctly, it is worthwhile to go over the input files MACH expects and their formats.
