Table 2:
Benchmark comparisons between 16GT and 5 other variant callers on a dataset from the Genome in a Bottle project consisting of 787M read pairs (53-fold) from genome NA12878.
| SNP | Indel | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FP | FP | |||||||||||
| Caller | Time (minutes w/36 cores) | TP | Total | dbSNP 138 | dbSNP 138% | TP in Omni 2.5 | FN | TP | Total | dbSNP 138 | dbSNP 138% | FN |
| 16GT | 121 | 2 663 179 | 5346 | 4220 | 79% | 20/20 | 918 | 167 549 | 1462 | 944 | 65% | 3180 |
| UG | 29 | 2 655 608 | 1639 | 563 | 34% | 15/15 | 8489 | 163 839 | 624 | 546 | 88% | 6890 |
| HC | 539 | 2 653 684 | 419 | 143 | 34% | 4/4 | 10 413 | 168 444 | 1232 | 726 | 59% | 2285 |
| Freebayes | 52 | 2 655 513 | 724 | 353 | 49% | 11/14 | 8584 | 162 505 | 559 | 0 | 0% | 8224 |
| Fermikit | 45 | 2 567 672 | 2036 | 509 | 25% | 9/9 | 96 425 | 161 916 | 1996 | 1076 | 54% | 8813 |
| ISAAC | 63 | 2 659 438 | 1115 | 586 | 53% | 15/15 | 4659 | 158 642 | 1239 | 710 | 57% | 12 087 |
| VarScan2 | 136 | 2 658 358 | 1680 | 718 | 43% | 10/10 | 5739 | 158 906 | 574 | 481 | 84% | 11 823 |
FP: false positive; FN: false negative; HC: GATK HaplotypeCaller; UG: GATK UnifiedGenotyper.