From: A study on fast calling variants from next-generation sequencing data using decision tree
 |  | Whole genome | ||||
---|---|---|---|---|---|---|
 |  | Fuwa | Platypus | GATK-UG | GATK-HC | SAMtools |
SNPs | 3,820,377 | 3,271,282 | 4,441,130 | 4,034,309 | 3,959,135 | |
Ti/tv | Â | 2.03 | 2.13 | 1.84 | 1.94 | 2.01 |
Axiom | GT concordance (%) | 99.32 | 98.29 | 97.3 | 98.52 | 99 |
Sensitivity (%) | 96.81 | 94.34 | 97.41 | 97.16 | 96.88 | |
Mono rate (%) | 0.04 | 0.13 | 0.22 | 0.11 | 0.07 | |
Fosmid | Recall (%) | 93.5 | 90.7 | 95.03 | 94.56 | 93.79 |
GIAB | Recall (%) | 98.41 | 89.34 | 98.65 | 98.44 | 97.89 |
Precision (%) | 99.26 | 99.69 | 97.72 | 98.79 | 99.47 | |
Indels | 649,387 | 575,350 | 711,045 | 884,204 | 765,800 | |
In-frame fraction | Â | 0.47 | 0.47 | 0.46 | 0.51 | 0.45 |
Fosmid | Recall (%) | 68.04 | 75.69 | 64.31 | 72.25 | 60.59 |
GIAB | Recall (%) | 87.48 | 69.49 | 89.74 | 94.7 | 80.98 |
Precision (%) | 95.93 | 78.49 | 95.59 | 94.08 | 92.32 | |
Runtime (real time, min) | 127 | 233 | 1058 | 2545 | 1546 |