Table 1.
Validation of variants by caller comparison
| Outcome | Intersection | UnifiedGenotyper only | HaplotypeCaller only |
|---|---|---|---|
| SNPs | |||
| Validated | 97 (98.0%) | 27 (96.4%) | 2 (22.2%) |
| Not validated | 2 (2.0%) | 1 (3.6%) | 7 (77.8%) |
| Fail | 3 | 0 | 1 |
| Total number of assays | 102 | 28 | 10 |
| Total number of working assays | 99 | 28 | 9 |
| INDELs | |||
| Validated | 35 (92.1%) | 11 (91.7%) | 3 (10.0%) |
| Not validated | 3 (7.9%) | 1 (8.3%) | 27 (90.0%) |
| Fail | 4 | 0 | 12 |
| Total number of assays | 42 | 12 | 42 |
| Total number of working assays | 38 | 12 | 30 |
The validation rates of LoF SNPs and INDEL calls from both methods (intersection) or uniquely called by UnifiedGenotyper or HaplotypeCaller. The failure rate of validation assays (fail) on the genotyping chip is given.