Changes

== FAQ  ==

== FAQ  ==

=== '''Q: Why and how to perform a 2-step imputation?''' ===

=== '''Why and how to perform a 2-step imputation?''' ===

A: When one has a large number of individuals (&gt;1000), we recommend a 2-step imputation to speed up. <br>  

A: When one has a large number of individuals (&gt;1000), we recommend a 2-step imputation to speed up. <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  

  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  

<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>  

===  '''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 HapMap III reference files? '''  

'''Q: Where can I find HapMap III reference files? '''