Table 4 Examples of VEP plugins
Plugin | Maintained by | Functionality |
|---|---|---|
CADD | Martin Kircher | Integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations |
dbNSFP | Ensembl | Provides pre-calculated scores from dbNSFP for many pathogenicity prediction tools for every possible missense variant in the human genome [96] |
dbscSNV | Ensembl | Retrieves data for splice variants from dbscSNV [97] |
ExAC | Ensembl | Retrieves ExAC allele frequencies from the Exome Aggregation Consortium (ExAC) project [32] |
GWAVA | Graham Ritchie | Predicts the functional impact of variants on non-coding elements from, e.g., ENCODE using GWAVA |
GXA | Ensembl | Reports data from the Expression Atlas |
LD | Ensembl | Finds variants in linkage disequilibrium with any overlapping existing variants |
LOFTEE | Konrad Karczewski | Predicts if stop gain, splice site, or frameshift variants lead to loss of function (LoF) in the affected protein |
MaxEntScan | Ensembl | Compares scores for reference and mutant splice site sequences using a maximum entropy method |
miRNA | Ensembl | Reports whether a variant is predicted to fall in a stem or loop region of a mature miRNA |
UpDownStream | Ensembl | By default the VEP searches 5Â kb either side of input variants for transcripts. Configures this distance which is useful in species with small intergenic distances or for investigating long-range trans-acting regulatory interactions |
VAX | Michael Yourshaw | Incorporates data from KEGG, Human Protein Atlas, MitoCarta, OMIM, and more into VEP output |