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MaCH

48 bytes added, 15:15, 18 May 2010
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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 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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== FAQ ==
'''Q: Why and how to perform a 2-step imputation?'''<br>
A: When one has a large number of individuals (&gt;1000), we recommend a 2-step imputation to speed up. <br>
&nbsp;&nbsp;&nbsp;&nbsp; A 2-step imputation contains the following 2 steps:<br>
&nbsp;&nbsp;&nbsp; (step 1) a representative subset of &gt;= 200 unrelated individuals are used to calibrate model parameters; and<br>&nbsp;&nbsp;&nbsp; (step 2) actual genotype imputation is performed for every person using parameters inferred in step 1. <br>  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Example command lines for a 2-step imputation:<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Example command lines for a 2-step imputation:<br>
mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer &gt; mach.infer.log
 <br>  mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip <br> --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails &gt; mach.imp.log
'''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>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The combined files should look like:<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''comb.ped'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; r1 r1 0 0 1 A/C C/C G/G G/A A/A<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 1 0 0 1 A/A ./. ./. G/G ./.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''comb.dat'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP2<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP3<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP4<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP5<br>
== Examples ==
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