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Table 1 Performance and runtimes on SMASH synthetic benchmark

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  
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  
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
  1. Best results are highlighted in boldface