Table 1 Comparison of different variant callers using real data on chromosome 21
From: vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
SNP | INDEL | |||||
|---|---|---|---|---|---|---|
Caller | Sensitivity (%) | Precision (%) | F1 score (%) | Sensitivity (%) | Precision (%) | F1 score (%) |
15 × | ||||||
vi-HMM | 95.11 | 99.62 | 97.31 | 91.95 | 90.18 | 91.06 |
FreeBayes | 94.82 | 91.61 | 93.18 | 88.93 | 74.79 | 81.25 |
Platypus | 90.97 | 99.84 | 95.20 | 93.74 | 70.03 | 80.17 |
SAMtools | 98.66 | 99.56 | 99.11 | 83.79 | 95.45 | 89.24 |
VarScan | 76.31 | 99.87 | 86.51 | 74.00 | 99.44 | 84.85 |
30 × | ||||||
vi-HMM | 99.81 | 99.44 | 99.63 | 95.22 | 95.62 | 95.42 |
FreeBayes | 95.80 | 95.48 | 95.64 | 90.36 | 76.41 | 82.80 |
Platypus | 92.92 | 99.73 | 96.21 | 95.67 | 69.54 | 80.54 |
SAMtools | 99.64 | 99.62 | 99.62 | 87.84 | 93.23 | 90.46 |
VarScan | 97.93 | 99.82 | 98.86 | 88.59 | 99.37 | 93.67 |
54 × | ||||||
vi-HMM | 99.95 | 99.18 | 99.56 | 95.61 | 96.09 | 95.85 |
FreeBayes | 95.88 | 96.90 | 96.39 | 90.77 | 77.27 | 83.48 |
Platypus | 92.97 | 99.63 | 96.18 | 96.06 | 69.11 | 80.38 |
SAMtools | 99.70 | 99.61 | 99.65 | 88.99 | 90.53 | 89.75 |
VarScan | 99.53 | 99.77 | 99.65 | 91.67 | 99.24 | 95.31 |