Table 5 Comparison of four variant callers on whole-exome sequencing data
From: A study on fast calling variants from next-generation sequencing data using decision tree
| Â | Â | Whole exome | ||||
|---|---|---|---|---|---|---|
| Â | Â | Fuwa | Platypus | GATK-UG | GATK-HC | SAMtools |
SNPs | 22,119 | 21,260 | 24,777 | 21,774 | 20,938 | |
Ti/tv | Â | 2.65 | 2.97 | 2.36 | 2.59 | 2.7 |
Axiom | GT concordance (%) | 96.82 | 92.83 | 90.83 | 95.65 | 97.15 |
Recall (%) | 91.09 | 86.55 | 92.37 | 90.34 | 89.8 | |
Mono rate (%) | 0.1 | 0.28 | 0.37 | 0.16 | 0.08 | |
Fosmid | Recall (%) | NA | NA | NA | NA | NA |
GIAB | Recall (%) | 87.59 | 77.39 | 87.02 | 86.37 | 86.78 |
Precision (%) | 98.44 | 99.88 | 93.06 | 96.28 | 97.61 | |
Indels | 478 | 773 | 405 | 440 | 680 | |
In-frame fraction | Â | 0.39 | 0.28 | 0.35 | 0.44 | 0.35 |
Fosmid | Recall (%) | NA | NA | NA | NA | NA |
GIAB | Recall (%) | 64.41 | 51.42 | 55.35 | 64.47 | 52.37 |
Precision (%) | 92.79 | 68.87 | 91.71 | 96.4 | 78.24 | |
Runtime (real time, min) | 13.5 | 9.8 | 93.6 | 170.5 | 85.3 | |