We developed a new statistical method (Supplementary Methods) to estimate the absolute copy number of each genotyped CNV, allowing us to distinguish deletions (0, 1 or 2 diploid copy number), duplications (2, 3 or 4 diploid copy number) and multiallelic CNVs (greater than 3 possible diploid copy numbers). Of the 5,238 genotyped CNVs, 77% were deletions, 16% were duplications and 7% were multi-allelic (Supplementary Fig. 1.1 and Supplementary Table 1.1). The 5:1 ratio of deletions to duplications probably partly reflects the greater technical challenge of robustly genotyping duplications.
