The Ensembl Variant Effect Predictor

William McLaren; Laurent Gil; Sarah E. Hunt; Harpreet Singh Riat; Graham R. S. Ritchie; Anja Thormann; Paul Flicek; Fiona Cunningham

doi:10.1186/s13059-016-0974-4

Table 1 Comparison of features of VEP with Annovar [95] and SnpEff [66]

From: The Ensembl Variant Effect Predictor

Class	Feature	VEP	Annovar	SnpEff
General	Language	Perl	Perl	Java
	Availability (non-commercial)	Free	Registration required	Free
	Availability (commercial)	Free	License required	Free
	Licence	Apache 2.0	Unspecified, not open source	LGPLv3
Input	VCF	Yes	Yes	Yes
	rsID	Yes	No	No
	HGVS	Yes	No	No
	BED	No	No	Yes
	Sequence variants	Yes	Yes	Yes
	Structural variants	Yes	Yes	Yes
Output	VCF	Yes	Yes (non-standard)	Yes
	HGVS	Yes	Yes	Yes
	Summary statistics	Yes	Yes	Yes
	Graphical summary	Yes	No	Yes
	Customizable output	Yes	No	No
Transcript sets	Ensembl	Yes	Yes	Yes
	RefSeq	Yes	Yes	Yes
	GENCODE Basic	Yes	Yes	No
	Species supported	~5000	94	~4500
	User-created databases	Yes	Yes	Yes
Interfaces	Local package	Yes	Yes	Yes
	Submission-based web interface	Ensembl Tools	wAnnovar	Galaxy
	Instant prediction web interface	Yes	No	No
	Cloud/VM	Yes	No	Yes
	API access	Perl, REST	No	No
Consequence types	Sequence Ontology	Yes	No	Yes
	Impact classification	Yes	No	Yes
	Number of classes	33	19	42
	Default reporting level	Transcript	Gene	Transcript
	Summary level reporting	Optional, customisable	Default, customisable	No
	Splicing predictions	Yes (via plugins)	Yes (via external data)	Yes (experimental)
	Loss of function prediction	Yes (via plugins)	No	Yes
	Nonsense mediate decay assessment	No	No	Yes
Non-coding	Regulatory features	Yes	Yes	Yes
	Support multiple cell lines	Yes	No	Yes
	TFBS scoring	Yes	No	No
	miRNA structure location	Yes (via plugins)	No	No
Known variants	Report known variants	Yes	Yes	Yes
	Filter by frequency	Yes	Yes	Yes
	Clinical significance	Yes	Yes	Yes
Other filters	Pre-set filters	Yes	Yes	Yes
Other filters	Arbitrary filtering	Yes	No	Yes
Other	Per-individual annotation	Basic	No	Somatic versus germline
	Annotation with custom data	Yes	Yes	Yes
	Custom code extensions via Plugin architecture	Yes	No	No

miRNA microRNA, TFBS transcription factor binding site, VM virtual machine

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