1. A method for determining a ploidy state of a chromosome or chromosome segment in the genome of a target individual, the method comprising: obtaining genetic data for the chromosome or chromosome segment from the target individual and from one or more related individuals; creating, on a computer, a set of at least one ploidy state hypothesis for the chromosome or chromosome segment of the target individual; using one or more expert techniques to determine, on a computer, for each expert technique used, a statistical probability for each ploidy state hypothesis in the set given the obtained genetic data, wherein at least one of the expert techniques is selected from the group consisting of techniques that determine the probability that a parental homolog is present or absent in the chromosome or chromosome segment in the target individual, techniques that normalize the genetic data for amplification bias between different loci or for amplification bias between different chromosomes, techniques that utilize the mean value of the genetic data on the chromosome or chromosome segment, techniques that utilize the cumulative distribution function (CDF) of different parental contexts for the genetic data on the chromosome or chromosome segment, and techniques that utilize genetic data for the X-transpose region in the X chromosome and Y chromosome; combining, on a computer, for each ploidy state hypothesis, the statistical probabilities as determined by the one or more expert techniques; and determining, on a computer, the ploidy state for the chromosome or chromosome segment in the genome of target individual based on the combined statistical probabilities of each of the ploidy state hypotheses.