Table 2 Comparison of the analytic performance of standard, clinical rWGS, and the 13.5-h method.
Variant type | Performance metric | NA12878 | NA24385 | ||||
|---|---|---|---|---|---|---|---|
Variant number | v.2.5 |
| Variant number | MC |
| ||
SNV | Precision | 3,258,654 | 99.8% | 99.9% | 3,440,606 | n.a. | 99.7% |
Recall | 99.7% | 99.9% | n.a. | 99.3% | |||
indel | Precision | 490,488 | 99.0% | 99.6% | 553,766 | n.a. | 99.4% |
Recall | 95.5% | 99.4% | n.a. | 98.6% | |||
SV deletion | Precision | n.a. | n.a. | n.a. | 4203 | 91.7% | 97.1% |
Recall | n.a. | n.a. | 57.3% | 61.7% | |||
SV insertion | Precision | n.a. | n.a. | n.a. | 5444 | 99.0% | 98.4% |
Recall | n.a. | n.a. | 27.4% | 49.3% | |||
CNV deletion | Precision | n.a. | n.a. | n.a. | 33 | 83.3% | 100.0% |
Recall | n.a. | n.a. | 9.1% | 87.9% | |||
- The analytic performance of DRAGEN v.3.7 (
) for SNVs and indels was compared with DRAGEN v2.5, the prior method, in reference samples NA12878 and NA24385, using NIST benchmark genotypes16. The analytic performance of DRAGEN v.3.7 for SVs and CNVs was compared with Manta and CNVnator (MC) in triplicate libraries in reference sample NA24385, using NIST benchmark genotypes. SV and CNV evaluations used Witty.Er, with default settings except event reporting [–em cts])35. SVs were of size >50 nt and CNVs >10 kb.
) for SNVs and indels was compared with DRAGEN v2.5, the prior method, in reference samples NA12878 and NA24385, using NIST benchmark genotypes