Table 3.

Summary of computational efficiency and user-friendliness over all approaches.

Software	Knowledge driven		Data driven
	AnnotSV	ClassifyCNV	CADD-SV	dbCNV	StrVCTVRE	SVScore	TADA	XCNV
Efficiency (second)	12	3	100 (20 cores)	38	19	5	16	24
Document quality	Excellent	Normal	Good	Normal	Good	Normal	Good	Good
Installation	cmd, conda, docker	cmd	conda	cmd	cmd, conda	cmd	cmd	cmd
Prerequisite dataset	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes
Genome build	hg19, hg38	hg19, hg38	hg38	hg19	hg19, hg38	hg19	hg19	hg19
Input	Bed, vcf	Bed	Bed	Bed	Bed	vcf	Bed	Bed
SV types	Deletion, insertion, duplication, inversion, breakend record	CNV	Deletion, insertion and duplication	CNV	Deletion, duplication	All types	CNV	CNV
Online webserver	Yes	No	Yes	No	Yes	No	No	Yes