We started with the exome capture array intervals plus the 100 bp of interval padding added during GATK processing but further restricted to the portion covered at ≥ 20× in all family members (with minimum base quality ≥ 10 and minimum map quality ≥ 20). The coverage threshold matches our threshold for de novo calling and the base and map quality thresholds correspond to the minimum considered by GATK during variant calling. We denote this interval “total callable” (see Table 1). We further defined the “total callable exome” (Table 1) as the intersection of this interval with the coding portion of the exome, according to RefSeq hg19 gene definitions (see previous section).
