LoFtool

Summary: A VEP plugin to add LoFtool scores Contributor(s): João Fadista Description: LoFtool provides a rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations for each gene in 60,706 individuals from Continue reading LoFtool

LOFTEE

Summary: A VEP plugin to identify LoF (loss-of-function) variation Contributor(s): Konrad Karczewski Description: LOFTEE (Loss-Of-Function Transcript Effect Estimator) is a plugin for the Ensembl Variant Effect Predictor (VEP) to identify LoF (loss-of-function) variation. It currently assesses variants that are: Stop-gained Splice site disrupting Continue reading LOFTEE

GWAVA

Summary: VEP plugin to get GWAVA scores Contributor(s): Graham Ritchie Description: GWAVA is a tool which aims to predict the functional impact of non-coding genetic variants based on a wide range of annotations of non-coding elements (largely from ENCODE/GENCODE), along with Continue reading GWAVA

VAX

Summary: VAX is a suite of VEP plugins Contributor(s): Michael Yourshaw Description: VAX is a suite of plugins for the Ensembl Variant Effect Predictor (VEP) to enrich its basic set of variant annotations with additional data on genes, function, conservation, expression, diseases, Continue reading VAX

dbNSFP

Summary: Retrieves scores from multiple pathogenicity predictors for missense variants Contributor(s): Will McLaren, Ensembl Description: This is a plugin for the Ensembl Variant Effect Predictor (VEP) that retrieves data for missense variants from a tabix-indexed dbNSFP file. Please cite the dbNSFP publication Continue reading dbNSFP

FATHMM

Summary: Retrieves FATHMM scores for variants Contributor(s): Will McLaren, Hashem Shihab, Ensembl Description: This is a plugin for the Ensembl Variant Effect Predictor (VEP) that gets FATHMM scores and predictions for missense variants. You will need the fathmm.py script and its Continue reading FATHMM

CADD

Summary: Retrieves CADD scores for variants Contributor(s): Will McLaren, Martin Kircher, Ensembl Description: This is a plugin for the Ensembl Variant Effect Predictor (VEP) that retrieves CADD scores for single nucleotide variants from a tabix-indexed CADD data file. Please cite the CADD Continue reading CADD

LD

Summary: Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases. Contributor(s): Graham Ritchie, Ensembl Description: This is a plugin for the Ensembl Variant Effect Predictor (VEP) that finds variants in linkage disequilibrium with any Continue reading LD

TSS Distance

Summary: A VEP plugin that calculates the distance from the transcription start site for upstream variants. Contributor(s): Graham Ritchie, Ensembl Description: Tested on Ensembl version(s): 65 Download URL: https://github.com/ensembl-variation/VEP_plugins/blob/master/TSSDistance.pm Licence: Ensembl