Birdsuite is also the first algorithm that takes a central idea of SNP analysis—that an empirical catalog of polymorphisms can be used to disentangle the problem of ab initio discovery from that of highly accurate measurement—and applies it to copy number analysis. For SNPs, discovery and genotyping use separate technologies and algorithms (sequencing and genotyping technology, respectively), but in copy number analysis, these problems have been treated as one: CNV ‘calls’ have been based on the results of genome-wide discovery algorithms. This can lead to false negatives and positives that might be tolerated in the creation of initial CNV catalogs, but that create tremendous problems in association studies that rely on accurate genotyping across large cohorts.
