Table 1 Variant loci counts from each tool
From: A genome-wide survey of mutations in the Jurkat cell line
| Â | GATK | Pindel | Breakdancer | CNVnator | Merged |
|---|---|---|---|---|---|
Substitutions | 3,520,988 | Â | Â | Â | 3,520,988 |
Short Hom. Deletion | 170,397 | Â | Â | Â | 170,397 |
Short Deletion | 841,001 | 1,239,299 | 47 | Â | 1,460,321 |
| Â | (70%) | (47%) | (0%) | Â | Â |
Short Insertion | 326,446 | 616,298 | Â | Â | 729,727 |
| Â | (65%) | (35%) | Â | Â | Â |
Long Hom. Deletion | 326 | Â | Â | 108 | 434 |
| Â | (0%) | Â | Â | (0%) | Â |
Long Deletion | 1904 | 118,610 | 6081 | 2499 | 125,397 |
| Â | (61%) | (1.4%) | (10%) | (1.2%) | Â |
Long Insertion | 1039 | 125,918 | 18 | Â | 126,657 |
| Â | (31%) | (0.25%) | (0%) | Â | Â |
Duplication | Â | 17,762 | Â | 1863 | 15,288 |
| Â | Â | (22%) | Â | (24%) | Â |
Inversion | Â | 149,545 | 183 | Â | 149,715 |
| Â | Â | (0.0087%) | (7.1%) | Â | Â |
Intra. Translocation | Â | Â | 1981 | Â | 1981 |
Inter. Translocation | Â | 4 | 113 | Â | 117 |
| Â | Â | (0%) | (0%) | Â | Â |