Table 2.

Variants and genotypes. Comparisons of variants and genotypes obtained in three samples using three target enrichment methods, two sequencing methods, and two alignment methods. The 50-hour WGS (STAT-Seq) was not enriched and used HiSeq 2500 sequencing. CMH-Dx1 was enriched for 523 genes and HiSeq 2000 sequencing. Average coverage of target nucleotides indicates the average aligned sequence depth over the corresponding target panel. For WGS, the target is the genome; for exome sequencing, the target is the exome; and for CMH-Dx1, the targets are 523 genes.

Sample	Target enrichment	Sequencing method	Alignment method	Sequence (GB)	Average coverage of target nucleotides	Variants detected by rapid WGS	Genotypes identical to both methods (%)
CMH064	Exome None (WGS)	HiSeq 2000 HiSeq 2500	GATK/GSNAP	9.8 12.1	79 40	46,756 (96.0%)	99.4
UDT173	CMH-Dx1 None (WGS)	HiSeq 2000 HiSeq 2500	GATK/GSNAP	4.1 13.9	784 46	1539 (96.7%)	99.60
UDT173	CMH-Dx1 None (WGS)	HiSeq 2000 HiSeq 2500	GATK/GSNAP CASAVA	4.1 13.9	784 46	1457 (83.0%)	99.9
UDT002	CMH-Dx1 None (WGS)	HiSeq 2000 HiSeq 2500	GATK/GSNAP CASAVA	4.2 13.3	770 44	1341 (76.6%)	99.5