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 genotype calls were 99.74% concordant with HapMap genotypes, approaching the estimated error rate of HapMap itself. Like previous algorithms, Birdseed is not without bias: minor-allele homozygotes are less well genotyped when the minor allele frequency is low, affecting both call rate and concordance of this class of genotypes. However, Birdseed compares favorably to the BRLMM algorithm1 (comparison done on Affymetrix 500K data, as BRLMM does not work on the Affymetrix SNP 6.0 array; see Supplementary Fig. 2 online). Birdseed as a stand-alone program has been used to genotype over 50,000 samples at the Broad Institute with an average call rate >99% (S.B.G., unpublished observations).
