|
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
|
