Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin

genome wide association study genomic life sciences loftee vep


VEP determines the effect of genetic variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. The European Bioinformatics Institute produces the VEP tool/db and releases updates every 1 - 6 months. The latest release contains 267 genomes from 232 species containing 5567663 protein coding genes. This dataset hosts the last 5 releases for human, rat, and zebrafish. Also, it hosts the required reference files for the Loss-Of-Function Transcript Effect Estimator (LOFTEE) plugin as it is commonly used with VEP.

Update Frequency

New packages are added as soon as they are available and confirmed to work with recent versions of Hail.


VEP use is governed by the Apache 2.0 licenses, and LOFTEE use is governed by the MIT license.


Managed By


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Usage Examples

Tools & Applications

Resources on AWS

  • Description
    VEP and LOFTEE data
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    AWS Region

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