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