Experimental validation was used to estimate and control the false discovery rates (FDR) for novel variants (Supplementary Table 3). The FDR for each complete called set was controlled to be less than 5% for SNPs and short indels, and less than 10% for structural variants (FDR for novel variants 2.6% for trio SNPs, 10.9% for low coverage SNPs, 1.7% for low coverage indels; further data in Supplementary Information and Supplementary Tables 3, 4a and 4b).
