Patent ID: 8359166

Claim:
A computer implemented method of generating genotype calls for a sample comprising: modeling, by a processor, allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation; transforming, by the processor, the allelic signals through the one or more model parameters of the allelic model to a normalized allelic space that serves to compensate for the one or more sources of systematic variation; determining, by the processor, a genotype for the sample based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model; creating, by the processor, a fixed prior probability distribution of normalized allele signals from a statistically significant training set of genotype data by fitting a normalized training set of genotype data to probability distributions that reflect a set of allowed genotypes in the normalized allelic space, wherein the probability distributions are based upon elliptical Gaussian probability distributions; and calling, by the processor, the genotype for the sample based upon a greatest prior probability as reflected by the fitted probability distribution and applied to the sample normalized in the normalized allelic space.