Table 3.
Validation rates of WGS-WES intersection, WGS-specific, and WES-specific INDELs
| INDELs | Valid | PPV | INDELs (>5 bp) | Valid (>5 bp) | PPV (>5 bp) | |
|---|---|---|---|---|---|---|
| WGS-WES intersection | 160 | 152 | 95.0% | 18 | 18 | 100% |
| WGS-specific | 145 | 122 | 84.1% | 33 | 25 | 75.8% |
| WES-specific | 161 | 91 | 56.5% | 1 | 1 | 100% |
We also calculated the validation rates of large INDELs (>5 bp) in each category. The validation rate, positive predictive value (PPV), is computed by the following: PPV = #TP/(#TP + #FP), where #TP is the number of true-positive calls and #FP is the number of false-positive calls.