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MaCH: Input Files

3 bytes removed, 11:30, 2 February 2017
Optional Phased Haplotypes
HapMap III phased haplotypes are in different format, you will need to use our converted haplotypes available at http://www.sph.umich.edu/csg/yli/mach/download/HapMap3.r2.b36.html
Additional reference files (e.g., those based on data from the 1000 Genomes Project; combined reference files) can be found through links at http://wwwcsg.sph.umich.edu/csg/yli/mach/download/
Phase haplotype information is encoded in two files. The first file (which MACH calls the "snp file") lists the markers in the phased haplotype. The second file (which MACH calls the "haplotype file") lists one haplotype per line. If you retrieved these files from the HapMap website, simply combine the --hapmapFormat option with the --snp option to indicate the name of the HapMap legend file and the --haps option to indicate the name of the file with phased haplotypes. Here is an example:
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