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MaCH

928 bytes added, 07:01, 18 May 2010
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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>
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 --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>
<br>
'''Q: Can I used unphased reference?'''<br>
A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br>
&nbsp;&nbsp;&nbsp;&nbsp; For example, if you have:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''ref.hap'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ACGGA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CCGAA
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''ref.snps'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SNP1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SNP2<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SNP3<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SNP4<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SNP5
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''sample.ped'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 1 0 0 1 A/A G/G&nbsp; <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''sample.dat'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M SNP4
&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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