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

Table 1 Structural variation callers used in SVMerge

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

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.

ISSN: 1474-760X