Fig. 2

CNV detection performance of each array using two different algorithms. a. Overlap of autosomal CNV calls from two different algorithms for each array platform with gold standard CNVs. Data is shown for each of two technical replicates per array. CNV call sets derived from the platform specific algorithm are in green, yellow, and red, and those derived from Nexus are in blue, pink, and purple. The number of array CNV calls overlapping a gold standard CNV by 50% reciprocally in size is in green and blue, by less than 50% reciprocally in size is in yellow and pink, and not overlapping a gold standard CNV is in red and purple. Array calls not overlapping a gold standard CNV at all were further analyzed for sequencing-based confirmation using CNVnator generated CNV calls based on the 1000 Genomes Project sequencing data for NA12878. The number of CNV calls not overlapping a gold standard CNV but with CNVnator support is shown as solid red or purple bars. The number of CNV calls not overlapping a gold standard CNV and with no CNVnator support is shown as hashed red or purple bars. b. Average rate of non-validated CNV calls for each array platform and for each algorithm. The rate of non-validated calls is calculated as the percentage of the total number of CNVs called from an array that do not overlap a gold standard CNV and do no have any supporting evidence from CNVnator (hashed red and purple bars in a.). Average rate of non-validated calls is based on two technical replicates