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