of a GSV in a cohort [19]. The initial (unsupervised) GSV detection was further improved by a series of manual procedures applied to each GSV locus under study: Only GSV calls covering at least 3 consecutive probes were considered; for short GSV regions spanning 6 or fewer probes, GSV calls were required to span the entire region; and SNP cluster plots were manually inspected to confirm both positive and negative GSV calls and to check for possible artefactual sources of differential GSV detection between cases and controls. For longer GSV regions (i.e. spanning ≥11 probes), it was also necessary to manage the effects of data noise or of the presence of a second small GSV in the same location on the homologous chromosome on GSV calling; a side-effect of the improved sensitivity of cnvHap is that, particularly for samples with lower data quality, larger GSVs are sometimes split into several smaller GSV calls. Thus, a modified procedure was employed: GSV calls across the entire region were combined, and individuals with copy number changes (i.e. deletion or duplication, as appropriate) at over 50% of probes within the region were provisionally called as carrying a GSV; the presence of a full-length GSV
