Table 1. Overview of how many causative variants out of 8,746 exonic were recovered on rank 1 and within the top 10 ranks by PVP and PVP-Human, and comparison to CADD, DANN, GWAVA, Exomiser eXtasy, and Phevor.
Analysis was performed on WES data. If a tool did not provide a score for a causative variant, we excluded the variant from this table; consequently, the total number of samples analyzed differs between the methods and the percentages reported are based on the number of samples for which the causative variant was ranked.
| Top hit (exonic) | Top 10 (exonic) | Total (exonic) | Median (exonic) | |
|---|---|---|---|---|
| CADD | 1,095 (15.15%) | 2,317 (32.05%) | 7,229 | 49 |
| DANN | 406 (6.06%) | 1,789 (26.69%) | 6,704 | 108 |
| GWAVA | 102 (1.41%) | 458 (6.32%) | 7244 | 339 |
| eXtasy | 553 (14.85%) | 1,601 (42.99%) | 3,724 | 19 |
| Exomiser | 2,156 (24.65%) | 5,122 (58.56%) | 8,746 | 5 |
| Phevor | 1,679 (28.25%) | 3,845 (64.70%) | 5,943 | 4 |
| PVP-Model | 4,007 (45.82%) | 6,353 (72.64%) | 8,746 | 2 |
| PVP-Human | 6,928 (79.21%) | 7,691 (87.94%) | 8,746 | 1 |
| PVP | 6,892 (78.80%) | 7,828 (89.50%) | 8,746 | 1 |