Table 1.
Accuracy and Efficiency Results on the HalfGenome and FullGenome Datasets
| Dataset | Tool | PSNP | RSNP | PINDEL | RINDEL | Time (hh:mm) | RAM (GB) |
|---|---|---|---|---|---|---|---|
| HalfGenome | MALVA | 93.8% | 91.1% | 86.0% | 81.4% | 04:33 | 30 |
| HalfGenome | VarGeno | 97.5% | 88.1% | 39.5% | 0.1% | 02:31 | 52 |
| HalfGenome | discoSnp++ | 89.5% | 39.3% | 80.8% | 24.2% | 07:45 | 7 |
| HalfGenome | BCFtools | 91.2% | 94.8% | 44.9% | 55.4% | 24:35 | 6 |
| HalfGenome | GATK | 91.7% | 95.1% | 53.2% | 79.9% | 34:43 | 32 |
| FullGenome | MALVA | 92.5% | 90.0% | 85.0% | 80.6% | 09:18 | 39 |
| FullGenome | VarGeno | – | – | – | – | – | – |
| FullGenome | discoSnp++ | 86.9% | 37.7% | 80.0% | 22.6% | 14:19 | 9 |
| FullGenome | BCFtools | 91.6% | 94.4% | 44.7% | 54.6% | 54:23 | 9 |
| FullGenome | GATK | 92.1% | 94.7% | 53.2% | 79.2% | 73:36 | 33 |
For each dataset, we reported the values of Precision (P) and Recall (R) obtained by the considered tools on both SNPs and indels. The efficiency results are shown in terms of wall clock time and peak memory usage. VarGeno could not complete the analysis of the FullGenome dataset; thus, we did not report its results on this dataset. See also Figure S1.