Quality control (QC) was done at the sample and anomaly level. Low quality samples (with high variance of BAF and/or LRR metrics or a high level of segmentation) were removed differentially for the two methods. Supplementary Table 1 shows the percentage of samples that passed QC for the BAF method (mean = 99.1%) and the LOH method (86.8%). In some studies, a high fraction of samples failed QC for LOH detection (maximum 47%), but the failure rates for BAF-detection (from which all mosaics were identified) are all low (maximum 8%). Anomaly-level QC involved several steps, including manual curation of all anomalies designated as mosaic and all other anomalies greater than 2 Mb in length. (see Supplementary Note). Manual curation involved evaluation of BAF/LRR plots, as shown in Figure 3 and Supplementary Fig. 2. Note that Supplementary Fig 2(m-t) shows a sample of eight of the smallest mosaic deletions. Features that distinguish mosaic from non-mosaic are described in the Figure 3 legend.
