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, 15:30, 20 May 2010
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− | [[Category:Software]]
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| [http://www.sph.umich.edu/csg/yli/mach/ '''MaCH'''] (MArkov Chain Haplotyping), mostly known as a software for genotype imputation, is a Hidden Markov Model (HMM) based haplotyper can that reconstruct haplotypes from genotypes of unrelated individuals. Three primary uses of MaCH are (1) to resolve haplotypes from diploid genotypes; (2) impute missing genotypes; and (3) perform disease mapping analysis. | | [http://www.sph.umich.edu/csg/yli/mach/ '''MaCH'''] (MArkov Chain Haplotyping), mostly known as a software for genotype imputation, is a Hidden Markov Model (HMM) based haplotyper can that reconstruct haplotypes from genotypes of unrelated individuals. Three primary uses of MaCH are (1) to resolve haplotypes from diploid genotypes; (2) impute missing genotypes; and (3) perform disease mapping analysis. |
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| Example command lines for a 2-step imputation:<br> | | Example command lines for a 2-step imputation:<br> |
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− | mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log
| + | #step 1: |
| + | mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log |
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− | <br>
| + | # step 2: |
| + | mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log |
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− | mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip
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− | --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log
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| '''Q: Where can I find combined HapMap reference files? '''<br> A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br> | | '''Q: Where can I find combined HapMap reference files? '''<br> A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br> |
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| mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.hap -r 100 -o phase | | mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.hap -r 100 -o phase |
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| + | [[Category:Software]] |