From: A study on fast calling variants from next-generation sequencing data using decision tree
 |  | benchmark | Fuwa | Platypus | GATK-UG | GATK-HC | SAMtools |
---|---|---|---|---|---|---|---|
a. NA24149 | |||||||
 non-dbSNPs | SNP | 235,880 | 300,076 | 473,231 | 644,589 | 568,941 | 543,132 |
Indel | 41,779 | 104,329 | 398,110 | 125,147 | 158,748 | 416,411 | |
 non-dbSNPs in benchmark | SNP | 235,880 | 234,135 | 230,167 | 235,362 | 235,506 | 234,330 |
Recall (%) | – | 99.26 | 97.58 | 99.78 | 99.84 | 99.34 | |
Precision(%) | – | 78.03 | 48.64 | 36.51 | 41.39 | 43.14 | |
Indel | 41,779 | 32,682 | 37,472 | 34,926 | 38,036 | 29,766 | |
Recall(%) | – | 78.23 | 89.69 | 83.60 | 91.04 | 71.25 | |
Precision (%) | – | 31.33 | 9.41 | 27.91 | 23.96 | 7.15 | |
b. NA24149 | |||||||
 non-dbSNPs | SNP | 235,889 | 306,323 | 486,914 | 659,433 | 582,136 | 551,555 |
Indel | 42,960 | 105,352 | 412,520 | 131,903 | 167,074 | 437,377 | |
 non-dbSNPs in benchmark | SNP | 235,889 | 233,881 | 230,076 | 235,251 | 235,477 | 234,184 |
Recall (%) | – | 99.15 | 97.54 | 99.73 | 99.83 | 99.28 | |
Precision(%) | – | 76.35 | 47.25 | 35.67 | 40.45 | 42.46 | |
Indel | 42,960 | 33,262 | 38,642 | 36,128 | 39,354 | 30,455 | |
Recall(%) | – | 77.43 | 89.95 | 84.10 | 91.61 | 70.89 | |
Precision (%) | – | 31.57 | 9.37 | 27.39 | 23.55 | 6.96 | |
c. NA24385 | |||||||
 non-dbSNPs | SNP | 235,666 | 337,194 | 405,643 | 420,580 | 335,917 | 510,292 |
Indel | 43,316 | 101,414 | 287,205 | 111,591 | 133,827 | 393,173 | |
 non-dbSNPs in benchmark | SNP | 235,666 | 234,975 | 216,620 | 235,010 | 235,227 | 234,147 |
Recall (%) | – | 99.71 | 91.92 | 99.72 | 99.81 | 99.36 | |
Precision(%) | – | 69.69 | 53.40 | 55.88 | 70.03 | 45.88 | |
Indel | 43,316 | 32,730 | 32,728 | 36,766 | 40,921 | 31,719 | |
Recall(%) | – | 75.56 | 75.56 | 84.88 | 94.47 | 73.23 | |
Precision (%) | – | 32.27 | 11.40 | 32.95 | 30.58 | 8.07 | |
d. NA24631 | |||||||
 non-dbSNPs | SNP | 238,105 | 279,070 | 339,514 | 426,948 | 353,943 | 344,006 |
Indel | 29,923 | 108,105 | 436,409 | 124,443 | 160,437 | 491,021 | |
 non-dbSNPs in benchmark | SNP | 238,105 | 236,336 | 232,361 | 237,545 | 237,664 | 236,804 |
Recall (%) | – | 99.26 | 97.59 | 99.76 | 99.81 | 99.45 | |
Precision(%) | – | 84.69 | 68.44 | 55.64 | 67.15 | 68.84 | |
Indel | 29,923 | 22,869 | 26,652 | 26,007 | 28,970 | 6885 | |
Recall(%) | – | 76.43 | 89.07 | 86.91 | 96.82 | 23.01 | |
Precision (%) | – | 21.15 | 6.11 | 20.90 | 18.06 | 1.40 |