Table 3 Performance and runtimes on GCAT Illumina 150× exome sequencing data
From: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
Caller | SNP calling (%) | Indel calling (%) | Time(s) | |||
|---|---|---|---|---|---|---|
| Â | Sensitivity | Specificity | T i /T v | Sensitivity | Specificity | Â |
SNVSniffer(M1) | 94.86 | 99.9982 | 2.223 | 50.48 | 99.9981 | 766 |
SNVSniffer(M2) | 94.86 | 99.9983 | 2.235 | 50.94 | 99.9981 | 931 |
SNVSniffer(M3) | 94.69 | 99.9982 | 2.251 | 50.94 | 99.9981 | 7597 |
SAMtools | 97.57 | 99.9989 | 1.450 | 43.08 | 99.9987 | 12825 |
GATK | 97.31 | 99.9982 | 1.920 | 95.28 | 99.9997 | 16568 |
FaSD | 79.83 | 99.9922 | 1.123 | − | − | 17986 |