Picard Tools (https://broadinstitute.github.io/picard/) generated capture, sequencing, alignment, and variant level quality metrics; and GATK DepthOfCoverage generated coverage metrics for the exome intervals (Table 1; Table S1). Principal components analysis (PCA) of these data focused on the first four principal components (PCs) to identify outliers (Figure S4). We considered samples greater than three standard deviations (SD) from the mean in any of the first four principal components as outliers and removed them from analysis. See next section for more details on the PCA.
