Table 2 Performance and runtimes on SMASH sampled human benchmark
From: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
Caller | NA12878 | NA12878+ | NA18507 | NA19240 |
|---|---|---|---|---|
Sensitivity (%) | Â | |||
SNVSniffer(M1) | 98.9 | 98.9 | 99.0 | 99.1 |
SNVSniffer(M2) | 98.9 | 98.9 | 98.9 | 99.0 |
SNVSniffer(M3) | 98.8 | 98.8 | 98.9 | 99.0 |
SAMtools | 99.2 | 99.2 | 99.3 | 99.4 |
GATK | 99.1 | 99.1 | 99.3 | 99.5 |
FaSD | 98.9 | 98.9 | 99.1 | 99.2 |
Time(s) | Â | |||
SNVSniffer(M1) | 226 | 203 | 190 | 206 |
SNVSniffer(M2) | 560 | 541 | 474 | 1065 |
SNVSniffer(M3) | 2550 | 2543 | 2093 | 3379 |
SAMtools | 3730 | 3694 | 3147 | 3379 |
GATK | 6541 | 6249 | 6321 | 5936 |
FaSD | 2132 | 2054 | 1979 | 2068 |