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 | ||||||
 Total | 3,600,577 | 4,596,629 | 4,936,516 | 5,078,361 | 4,962,252 | 5,121,162 |
 SNP | 3,062,103 | 3,773,197 | 3,741,864 | 4,222,373 | 4,073,476 | 4,052,727 |
 Indel | 538,474 | 823,432 | 1,194,652 | 855,988 | 888,776 | 1,068,435 |
 SNP Recall(%) | – | 99.64 | 94.10 | 99.88 | 99.88 | 99.55 |
 SNP Precision(%) | – | 80.86 | 77.00 | 72.44 | 75.08 | 75.22 |
 Indel Recall(%) | – | 91.99 | 97.26 | 95.51 | 96.66 | 80.30 |
 Indel Precision(%) | – | 60.16 | 43.84 | 60.08 | 58.57 | 40.47 |
b. NA24143 | ||||||
 Total | 3,638,487 | 4,683,584 | 5,047,869 | 5,185,325 | 5,069,960 | 5,231,986 |
 SNP | 3,089,689 | 3,848,083 | 3,818,763 | 4,304,521 | 4,153,126 | 4,127,152 |
 Indel | 548,798 | 835,501 | 1,229,106 | 880,804 | 916,834 | 1,104,834 |
 SNP Recall(%) | – | 99.65 | 94.12 | 99.89 | 99.90 | 99.55 |
 SNP Precision(%) |  | 80.01 | 76.15 | 71.70 | 74.32 | 74.53 |
 Indel Recall(%) | – | 91.86 | 97.29 | 95.73 | 96.92 | 80.38 |
 Indel Precision(%) |  | 60.34 | 43.44 | 59.64 | 58.01 | 39.92 |
c. NA24385 | ||||||
 Total | 3,650,031 | 4,765,697 | 4,425,266 | 4,839,691 | 4,685,838 | 5,191,731 |
 SNP | 3,101,709 | 3,942,411 | 3,452,047 | 3,987,637 | 3,803,199 | 4,123,595 |
 Indel | 548,322 | 823,286 | 973,219 | 852,054 | 882,639 | 1,068,136 |
 SNP Recall(%) | – | 99.91 | 88.60 | 99.88 | 99.92 | 99.67 |
 SNP Precision(%) |  | 78.60 | 79.60 | 77.69 | 81.49 | 74.97 |
 Indel Recall(%) | – | 91.39 | 90.14 | 95.98 | 98.21 | 81.96 |
 Indel Precision(%) |  | 60.87 | 50.79 | 61.77 | 61.01 | 42.07 |
d. NA24631 | ||||||
 Total | 3,655,030 | 4,599,648 | 4,935,176 | 4,987,136 | 4,871,278 | 4,667,766 |
 SNP | 3,195,050 | 3,743,038 | 3,647,691 | 4,079,102 | 3,901,018 | 3,900,109 |
 Indel | 459,980 | 856,610 | 1,287,485 | 908,034 | 970,260 | 767,657 |
 SNP Recall(%) | – | 99.48 | 93.98 | 99.93 | 99.92 | 99.67 |
 SNP Precision(%) |  | 84.92 | 82.32 | 78.27 | 81.84 | 81.65 |
 Indel Recall(%) | – | 93.52 | 97.53 | 97.53 | 99.54 | 12.48 |
 Indel Precision(%) |  | 50.22 | 34.84 | 49.41 | 47.19 | 7.48 |