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

genome wide association study genomic life sciences loftee vep

Description

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.

License

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

Documentation

https://hail-vep-pipeline.public.tennex.io/

Managed By

Tennex

See all datasets managed by Tennex.

Contact

https://www.tennex.io/contact

How to Cite

Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin was accessed on DATE from https://registry.opendata.aws/hail-vep-pipeline.

Usage Examples

Tools & Applications

Resources on AWS

  • Description
    VEP and LOFTEE data
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::hail-vep-pipeline
    AWS Region
    us-east-1
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://hail-vep-pipeline/

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