The method of anomaly detection is described in detail in the Supplementary Note and summarized here. Detection of anomalies (both mosaic and non-mosaic) was based on BAF and LRR metrics. The primary focus for detecting anomalies was BAF, because we wanted to identify copy-neutral events (mosaic UPD) and because BAF is much less noisy and prone to artifacts (such as GC waves48) than LRR. The main approach was to detect a split in the BAF intermediate band, which in normal (biparental disomic) samples is centered at 1/2 and corresponds to AB heterozygotes (Figure 1). In trisomic samples, this band splits into two components (AAB and ABB) at BAF= 1/3 and 2/3. In disomic-trisomic mosaics, the width of the split varies from zero to one third and LRR varies from zero to a theoretical value of log2(3/2). In disomic-monosomic mosaics, the width of the split varies from zero to one and LRR varies from 0 to a theoretical value of log2(1/2). In biparental-uniparental disomic mosaics, the width of the split varies from zero to one, while LRR remains constant at zero.
