Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin Dataset for Machine Learning
Install DagsHub:
pip install dagshubTo stream this data directly on DagsHub
from dagshub.streaming import DagsHubFilesystem
fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/hail-vep-pipeline-dataset")
fs.listdir("s3://hail-vep-pipeline")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.
Additional information
Documentation
Update frequency
New packages are added as soon as they are available and confirmed to work with recent versions of Hail.