The Birdsuite is 4-part framework, that first genotypes (calls discrete copy number) of known CNPs, then calls SNP genotypes (for samples and SNPs believed to have 2 copies of the locus) and builds batch- and locus-specific models of probe characteristics, then searches for novel CNVs, and finally integrates these together to provide mutually informed and consistent sequence- and copy-number-genotypes at each locus for each sample.
Genotypes common copy-number polymorphisms (CNPs)
Genotypes SNPs using the classical AA, AB, and BB genotypes
Detects Rare/de novo copy-number variants (CNVs)
Integrates CNV information to produce mutually consistent SNP genotypes (i.e. including genotypes such as A-null and AAB)