Call set | Deletion | Insertion | Inversion | CNG | Complexa | Total |
|---|
BDMax | 4,141 | 1,844 | 324 | - | - | 6,309 |
Pindel | 458 | 0 | - | - | - | 458 |
SECluster | - | 1,215 | - | - | - | 1,215 |
RetroSeq | - | 2,297 | - | - | - | 2,297 |
RDXplorer | 575 | - | - | 280 | - | 855 |
Merged raw | 4,717 | 5,252 | 324 | 280 | - | 10,573 |
SVMerge final | 4,184 | 575 | 38 | 280 | 99 | 5,176 |
- a'Complex' refers to any locus with more than one structural variant type - for example, an inversion with a deletion. Shown are the numbers of raw calls (>100 bp) from each structural variation (SV) caller, filtered by score and location only (see Materials and methods), for NA18506, the child in the HapMap trio dataset. 'BDMax' is BreakDancerMax. Pindel is able to identify deletions that also contain small insertions; these are included in the total deletion count. 'Merged raw' is the resulting number of calls after merging of these calls by their coordinates (see Materials and methods). 'SVMerge final' is the total number of calls made after refinement of the SV call list by local assembly and read depth analysis. Copy number gains (CNG) are not subject to validation by local assembly.
