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Table 3 Structural variant calls for individual NA18506

From: Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

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
  1. 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.