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MaCH (view source)

Revision as of 08:34, 26 November 2010

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MACH
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'''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.
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'''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.
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This page includes links to several useful MaCH related resources.  
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== Options ==
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* The main MaCH webpage at http://www.sph.umich.edu/csg/abecasis/MaCH/
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* The MaCH download page, with source code, executables and reference haplotype files at http://www.sph.umich.edu/csg/abecasis/MaCH/download/
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* The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/
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* [[MaCH FAQ|The MaCH FAQ]]
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* [[MaCH Options|MaCH Options]]
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* [[MaCH: Input Files|Information on MaCH input formats]]
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* [[MaCH: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation Cookbook]]
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* [[MaCH: machX|Chromosome X Imputation]]
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* [[Mach2dat: Association with MACH output]]
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Input Files:
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Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!
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--datfile
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Marker information file for subjects under study.
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--pedfile
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Pedigree file for subjects under study.
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[[Category:Software]]
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== FAQ ==
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Q: Where can I find combined HapMap reference files?
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A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html
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Q: Where can I find HapMap III reference files?
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A: http://www.sph.umich.edu/csg/yli/mach/download/
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Q: Does --mle overwrite fed-in genotypes?
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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.
 
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