Table 1.

SV detection methods and example SV callers

Method	Detection resolution	Detectable SV types	Detectable SV sizes	Example SV callers	References
Read-pair	Rough	All	Median size SV	BreakDancer	Chen et al. [14]
Split-read	Base pair	All	Small size SV	Pindel	Ye et al. [24]
Read-pair and split-read	Base pair	All	Depend on filtering/scoring	Delly	Rausch et al. [29]
				Lumpy	Layer et al. [30]
Read-pair, split-read and local-assembly	Base pair	All	Depend on filtering/scoring	Manta	Chen et al. [33]
				GRIDSS	Cameron et al. [26]
				SvABA	Wala et al. [27]