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== FAQ ==
== FAQ ==
'''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>
Q: Where can I find HapMap III reference files? <br> A: http://www.sph.umich.edu/csg/yli/mach/download/ <br><br>
'''Q: Where can I find HapMap III reference files? '''<br> A: http://www.sph.umich.edu/csg/yli/mach/download/ <br><br>
Q: Does --mle overwrite fed-in genotypes?<br> A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.<br><br>
'''Q: Does --mle overwrite fed-in genotypes?'''<br> A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.<br><br>
Q: How do I get reference files for an region of interest? <br>
'''Q: How do I get reference files for an region of interest? '''<br> A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br>
A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br>
(2) For MACH format, you can do the following:
(2) For MACH format, you can do the following:
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
<br>Q: Do I have to sort the pedigree file by physical positions? <br>
<br>'''Q: Do I have to sort the pedigree file by physical positions? '''<br> A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br>
A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br>
<br>Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? <br>
<br>'''Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''<br> A: mach automatically resets it to maximum possible value.
A: mach automatically resets it to maximum possible value.
<br>
'''Q: Can I used unphased reference?'''<br>
A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br>
For example, if you have:
'''ref.hap'''<br> ACGGA<br> CCGAA
'''ref.snps'''<br> SNP1<br> SNP2<br> SNP3<br> SNP4<br> SNP5
'''sample.ped'''<br> 1 1 0 0 1 A/A G/G <br>
'''sample.dat'''<br> M SNP1<br> M SNP4
The combined files should look like:<br> '''comb.ped'''<br> r1 r1 0 0 1 A/C C/C G/G G/A A/A<br> 1 1 0 0 1 A/A ./. ./. G/G ./.
'''comb.dat'''<br> M SNP1<br> M SNP2<br> M SNP3<br> M SNP4<br> M SNP5<br>
== Examples ==
== Examples ==
