From: A study on fast calling variants from next-generation sequencing data using decision tree
AF | Â | benchmark | Fuwa | Platypus | GATK-UG | GATK-HC | SAMtools |
---|---|---|---|---|---|---|---|
a. NA24149 | |||||||
  ≤ 5% | Count | 182,482 | 179,986 | 174,392 | 181,248 | 181,586 | 179,514 |
Recall (%) | – | 98.63 | 95.57 | 99.32 | 99.51 | 98.37 | |
  ≤ 1% | Count | 72,585 | 71,636 | 69,736 | 72,098 | 72,090 | 71,434 |
Recall (%) | – | 98.69 | 96.07 | 99.33 | 99.32 | 98.41 | |
  ≤ 0.5% | Count | 54,448 | 53,757 | 52,379 | 54,096 | 54,041 | 53,603 |
Recall (%) | – | 98.73 | 96.20 | 99.35 | 99.25 | 98.45 | |
  ≤ 0.1% | Count | 32,831 | 32,473 | 31,607 | 32,637 | 32,567 | 32,402 |
Recall (%) | – | 98.91 | 96.27 | 99.41 | 99.20 | 98.69 | |
  = 0% (novel) | Count | 298,984 | 265,501 | 285,754 | 282,165 | 282,348 | 211,935 |
Recall(%) | – | 88.80 | 95.58 | 94.37 | 94.44 | 70.89 | |
b. NA24143 | |||||||
  ≤ 5% | Count | 189,494 | 187,013 | 180,969 | 188,308 | 188,644 | 186,607 |
Recall (%) | – | 98.69 | 95.50 | 99.37 | 99.55 | 98.48 | |
  ≤ 1% | Count | 74,701 | 73,773 | 71,681 | 74,253 | 74,215 | 73,646 |
Recall (%) | – | 98.76 | 95.96 | 99.40 | 99.35 | 98.59 | |
  ≤ 0.5% | Count | 55,428 | 54,744 | 53,241 | 55,104 | 55,023 | 54,664 |
Recall (%) | – | 98.77 | 96.05 | 99.42 | 99.27 | 98.62 | |
  ≤ 0.1% | Count | 33,113 | 32,711 | 31,816 | 32,918 | 32,831 | 32,705 |
Recall (%) | – | 98.79 | 96.08 | 99.41 | 99.15 | 98.77 | |
  = 0% (novel) | Count | 304,746 | 269,764 | 291,681 | 288,547 | 288,978 | 215,956 |
Recall(%) | – | 88.52 | 95.71 | 94.68 | 94.83 | 70.86 | |
c. NA24385 | |||||||
  ≤ 5% | Count | 187,589 | 185,929 | 163,225 | 186,412 | 186,909 | 185,048 |
Recall (%) | – | 99.12 | 87.01 | 99.37 | 99.64 | 98.65 | |
  ≤ 1% | Count | 74,132 | 73,539 | 64,827 | 73,693 | 73,720 | 73,241 |
Recall (%) | – | 99.20 | 87.45 | 99.41 | 99.44 | 98.80 | |
  ≤ 0.5% | Count | 55,153 | 54,748 | 48,305 | 54,851 | 54,811 | 54,551 |
Recall (%) | – | 99.27 | 87.58 | 99.45 | 99.38 | 98.91 | |
  ≤ 0.1% | Count | 32,722 | 32,516 | 28,673 | 32,547 | 32,487 | 32,443 |
Recall (%) | – | 99.37 | 87.63 | 99.47 | 99.28 | 99.15 | |
  = 0% (novel) | Count | 303,456 | 267,728 | 259,920 | 289,030 | 294,058 | 222,433 |
Recall(%) | – | 88.23 | 85.65 | 95.25 | 96.90 | 73.30 | |
d. NA24631 | |||||||
  ≤ 5% | Count | 241,718 | 239,035 | 230,265 | 240,706 | 241,089 | 222,774 |
Recall (%) | – | 98.89 | 95.26 | 99.58 | 99.74 | 92.16 | |
  ≤ 1% | Count | 112,774 | 111,568 | 108,087 | 112,284 | 112,308 | 104,437 |
Recall (%) | – | 98.93 | 95.84 | 99.57 | 99.59 | 92.61 | |
  ≤ 0.5% | Count | 88,884 | 87,972 | 85,370 | 88,521 | 88,467 | 82,493 |
Recall (%) | – | 98.97 | 96.05 | 99.59 | 99.53 | 92.81 | |
  ≤ 0.1% | Count | 47,358 | 46,889 | 45,557 | 47,135 | 47,045 | 44,078 |
Recall (%) | – | 99.01 | 96.20 | 99.53 | 99.34 | 93.07 | |
  = 0% (novel) | Count | 231,303 | 208,579 | 220,259 | 224,747 | 227,952 | 66,392 |
Recall(%) | – | 90.18 | 95.23 | 97.17 | 98.55 | 28.70 |