nts detected by rapid WGS (using the HiSeq 2500 and CASAVA) and targeted sequencing (using exome enrichment, the HiSeq 2000, and GATKIGSNAP)-99.5% (UDT002), 99.9% (UDT173), and 99.7% (CMH064) (Table 2)—further indicating that rapid WGS is highly con- cordant with an established genotyping method (33).

—19 days. In contrast, rapid WGS did not use target enrichment, was performed with the HiSeq 2500 instrument, and took —50 hours. Samples CMH064, UDT002, and UDTI73 were sequenced using these three methods, and variants were detected with a single alignment method [the Genomic Short-read Nucleotide