design, suffer from low probe coverage and cross-hybridization, and they are therefore often refractory to CNV detection using array-based techniques. Indeed, CNVs overlapping SegDups generally have fewer probes supporting them (Supplementary Fig. 7) and their reproducibility is lower compared to CNVs in unique sequence. Another contributing factor influencing the reproducibility of large CNVs is call fragmentation, that is, a single CNV is detected as multiple smaller variants. After lowering the minimum overlap required for a call to be considered replicated from 80% to any overlap, the reproducibility of large calls increases (Supplementary Table 4). Taken together, these factors likely offset the benefit of the increased number of probes in larger CNVs for call reproducibility.
