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Table 1 Structural variation callers used in SVMerge

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

Software Analysis method SV types called Size detection limitations
BDMax Paired-end mapping D, I, Inv, T Insertions limited by library insert size
Pindel Split-mapping D, I, D+I Insertions limited by read size; deletions <1 Mb
SECluster Clusters of one-end-mapped reads I Minimum size dependent on insert size
RetroSeq Targeted insertion calling RI Minimum size dependent on insert size
RDXplorer Read depth D, G Minimum size approximately 1 kb
  1. Listed are the software used to call structural variants (SVs), the analysis method used, SV types called, and limitations of the SV caller. 'BDMax' is BreakDancerMax. D, deletion; D+I, deletion with small insertion; G, copy number gain; I, insertion; Inv, inversion; RI, repeat insertion; T, translocation.