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== FAQ ==
== FAQ ==
Q: Where can I find combined HapMap reference files?
A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html
Q: Where can I find HapMap III reference files?
A: http://www.sph.umich.edu/csg/yli/mach/download/
Q: 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.
