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