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== FAQ ==
== FAQ ==
=== '''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 (>1000), we recommend a 2-step imputation to speed up. <br>
A: When one has a large number of individuals (>1000), we recommend a 2-step imputation to speed up. <br>
# step 2:
# step 2:
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 > 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 > mach.imp.log
===
=== '''Where can I find combined HapMap reference files? ''' ===
A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br>
A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br>
=== '''Where can I find HapMap III / 1000 Genomes reference files? ''' ===
=== '''Where can I find HapMap III / 1000 Genomes reference files? ''' ===
A: http://www.sph.umich.edu/csg/yli/mach/download/ <br>
A: http://www.sph.umich.edu/csg/yli/mach/download/ <br>
=== '''Does --mle overwrite fed-in genotypes?''' ===
=== '''Does --mle overwrite fed-in genotypes?''' ===
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>
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>
=== '''How do I get imputation quality estimates?''' ===
=== '''How do I get imputation quality estimates?''' ===
A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout:
A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout:
<br>
<br>
=== '''How do I get reference files for an region of interest? ''' ===
=== '''How do I get reference files for an region of interest? ''' ===
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>
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
===
=== '''Do I have to sort the pedigree file by physical positions? ''' ===
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>
=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? ''' ===
=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? ''' ===
A: mach automatically resets it to maximum possible value.
A: mach automatically resets it to maximum possible value.
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<br>
=== '''Can I used unphased reference?''' ===
=== '''Can I used unphased reference?''' ===
A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br>
A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br>
