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

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

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