Birdsuite is qualitatively different from previous algorithms in that it approaches SNP genotyping and copy number analysis as a problem of joint estimation in which the sequence and copy number aspects of data analysis inform one another. Although we developed the Birdsuite to make use of data generated by a specific SNP and CNP genotyping array, the concepts and approach described here represent a general strategy that can be applied to any genotyping platform. The approach is model-based and empirically derived, offering a sensitive and mutually consistent description of sequence variation, and substantially reducing apparent errors (of mendelian inheritance and Hardy-Weinberg equilibrium) that actually reflect a true state of the individual’s genomic sequence.
