Changes

[[Minimac]] runs are controled by a series of command line parameters that specify input file names, an initial model for recombination and error rates, an optional series of iterations of model refinement using either [[Monte-Carlo]] methods or an [[Expectation-Maximization]] algorithm, and output file names.

[[Minimac]] and [[Minimac2]] runs are controled by a series of command line parameters that specify input file names, an initial model for recombination and error rates, an optional series of iterations of model refinement using either [[Monte-Carlo]] methods or an [[Expectation-Maximization]] algorithm, and output file names.

== Reference Haplotype Set ==

== Reference Haplotype Set ==