SNP genotyping is done using Birdseed (see Supplementary Methods and the BirdSuite web site), a specialized two-dimensional GMM, where the two dimensions are summarized probe intensities for each of the two alleles (A and B). Like Canary, Birdseed utilizes prior models representing the expected allele intensity information for each genotype class, built from previous data for samples of known genotype at each SNP (in this case, 270 HapMap samples and genotypes). Briefly, the algorithm utilizes expectation-maximization14 to determine the location of the AA, AB and BB clusters for each SNP (Fig. 3c and Supplementary Fig. 1 online). These clusters are used to assign a genotype (AA, AB or BB) to each sample along with a score reflecting the confidence of each call. Special procedures are used on the X, Y and mitochondrial chromosomes. Birdseed performance was validated on HapMap samples run on the Affymetrix SNP 6.0 array6 across seven different labs, not including any experiments used to generate the models or develop the algorithm. At the default confidence threshold, call rate on the HapMap samples was 99.47%, and these confident
