There are multiple algorithms that can be used for calling CNVs, and many are specific to certain array types. We decided to perform CNV calling with the algorithms recommended by each array producer, as well as several additional established methods. In total, 11 different algorithms were used to call CNVs for different subsets of the data (Table 1). The settings applied for these algorithms reflect parameters typically used in research laboratories, with a minimum of 5 probes and a minimum size of 1kb to call a CNV (see Supplementary Methods for settings used for each analysis tool).
