From: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
Caller | SNP calling (%) | Indel calling (%) | Time(s) | ||||
---|---|---|---|---|---|---|---|
 | Recall | Precision | F-score | Recall | Precision | F-score |  |
Venter | Â | ||||||
SNVSniffer(M1) | 98.5 | 97.1 | 97.8 | 68.9 | 83.0 | 75.3 | 133 |
SNVSniffer(M2) | 98.3 | 97.4 | 97.8 | 69.0 | 83.7 | 75.6 | 320 |
SNVSniffer(M3) | 97.9 | 98.5 | 98.2 | 70.4 | 83.6 | 76.4 | 1331 |
SAMtools | 98.3 | 97.1 | 97.7 | 63.7 | 69.5 | 66.5 | 2046 |
GATK | 98.1 | 99.1 | 98.6 | 76.2 | 86.2 | 80.9 | 2538 |
FaSD | 98.0 | 97.5 | 97.7 | − | − | − | 2005 |
Contaminated venter | Â | ||||||
SNVSniffer(M1) | 98.0 | 97.4 | 97.7 | 69.0 | 84.0 | 75.8 | 119 |
SNVSniffer(M2) | 97.8 | 97.8 | 97.8 | 68.7 | 84.5 | 75.8 | 336 |
SNVSniffer(M3) | 97.3 | 98.7 | 98.0 | 69.7 | 84.3 | 76.3 | 1387 |
SAMtools | 98.1 | 97.3 | 97.7 | 62.7 | 72.1 | 67.1 | 2046 |
GATK | 97.9 | 96.8 | 97.3 | 75.8 | 86.4 | 80.8 | 2803 |
FaSD | 97.4 | 97.5 | 97.4 | − | − | − | 2070 |