Difference between revisions of "MaCH"

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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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'''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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== Options ==
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This page includes links to several useful MaCH related resources.
  
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Input Files:
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* The main MaCH webpage at http://www.sph.umich.edu/csg/abecasis/MaCH/
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--datfile
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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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Marker information file for subjects under study.
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* The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/
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--pedfile
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* [[MaCH FAQ|The MaCH FAQ]]
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Pedigree file for subjects under study.
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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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Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!
  
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== FAQ ==
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[[Category:Software]]
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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.
 

Latest revision as of 08:34, 26 November 2010

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 (Scott et al, Science, 2007) and has since been used in the analysis of many other GWAS.

This page includes links to several useful MaCH related resources.

Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=MaCH&oldid=2559"