Table 2.
Variant validation of default TVC output (VCF1) against NA12878 truth set.
| Total Variants | Truth set | TPs | FNs | FPs | Sensitivity | PPV | |
|---|---|---|---|---|---|---|---|
| AmpliSeq | |||||||
| Total Variants | 54,351 | 49,340 | 45,946 | 3,394 | 8,405 | 93.12% | 84.54% |
| Total SNVs | 50,913 | 45,092 | 43,840 | 1,252 | 7,073 | 97.22% | 86.11% |
| Exonic SNVs | 19,650 | 16,964 | 16,588 | 376 | 3,062 | 97.78% | 84.42% |
| Total Indels | 3,436 | 4,248 | 2,106 | 2,142 | 1,330 | 49.58% | 61.29% |
| Exonic indels | 539 | 329 | 231 | 98 | 308 | 70.21% | 42.86% |
| SureSelect | |||||||
| Total Variants | 54,934 | 46,982 | 43,929 | 3,053 | 11,005 | 93.50% | 79.97% |
| Total SNVs | 52,013 | 43,367 | 42,230 | 1,137 | 9,783 | 97.38% | 81.19% |
| Exonic SNVs | 19,171 | 16,120 | 15,846 | 274 | 3,325 | 98.30% | 82.66% |
| Total Indels | 2,921 | 3,614 | 1,699 | 1,915 | 1,222 | 47.01% | 58.17% |
| Exonic indels | 312 | 277 | 195 | 82 | 117 | 70.40% | 62.50% |
Truth set—Variants in v3.3.2 of high-confidence calls VCF of NA12878 from Genome in the Bottle project, SNVs,Single Nucleotide Variants; TPs,True Positives; FNs, False Negatives; FPs, False Positives; PPV, Positive Predictive Value; TVC, Torrent Variant Caller, VCF1—This corresponds to Figure 1 .