The utility of genotypes from the Birdsuite, however, is not realizable unless analysis tools can accept and evaluate CNVs and noncanonical SNP genotypes, and test them for association with phenotype in a statistically robust manner. Specifically, in addition to performing the typical SNP test of association, one needs to assess the potential relationship of phenotypes to total copy number and allele-specific copy number (for example, AAB versus ABB). For example, a locus may be haploinsufficient when the remaining copy carries a low-expression allele, but not linked to the phenotype if the remaining copy is a high-expression allele. It is also important to assess association of phenotype with a collection of individually rare CNVs that overlie a common locus.
