Table 2.
Quality evaluation of variant detection using different variant-calling pipelines.
| Sensitivity | Specificity | |||
|---|---|---|---|---|
| Mean* | SD | Mean* | SD | |
| SOAPsnp | 94.68 | 2.26 | 99.79 | 0.03 |
| GATK1.5 | 95.34 | 1.16 | 99.72 | 0.08 |
| SNVer | 92.33 | 4.40 | 99.78 | 0.04 |
| GNUMAP | 86.60 | 3.23 | 99.64 | 0.06 |
| SAMtools | 94.47 | 4.22 | 99.59 | 0.16 |
| Any pipeline | 97.67 | 1.20 | 99.62 | 0.11 |
| ≥ 2 pipelines* | 96.64 | 2.28 | 99.69 | 0.07 |
| ≥ 3 pipelines* | 95.62 | 3.13 | 99.73 | 0.05 |
| ≥ 4 pipelines* | 92.60 | 3.40 | 99.82 | 0.04 |
| 5 pipelines* | 80.58 | 5.26 | 99.87 | 0.01 |
*Intersection of variants contained in the number of pipelines specified.
Sensitivity and specificity was calculated for each pipeline by comparing Illumina Human610-Quad version 1 SNP arrays with exome-capture sequencing results, based on the four samples whose genotyping data was available.