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MaCH

6 bytes added, 08:01, 18 May 2010
FAQ
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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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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