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

Stream data with DDA:

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.

Contact:

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.

Managed By:

https://www.tennex.io/

Resources:

1. resource:
   • Description: VEP and LOFTEE data
   • ARN: arn:aws:s3:::hail-vep-pipeline
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, genome wide association study, genomic, life sciences, vep, loftee

Tools & Applications:

1. tools & applications:

   • Title: Hail
   • URL: https://hail.is/
   • AuthorName: Neale Lab
   • AuthorURL: https://www.nealelab.is/

2. tools & applications:

   • Title: Variant Effect Predictor (VEP)
   • URL: http://uswest.ensembl.org/info/docs/tools/vep/index.html
   • AuthorName: Ensembl
   • AuthorURL: http://uswest.ensembl.org/info/docs/tools/vep/index.html

3. tools & applications:

   • Title: Loss-Of-Function Transcript Effect Estimator (LOFTEE)
   • URL: https://github.com/konradjk/loftee
   • AuthorName: Konrad Karczewski
   • AuthorURL: https://github.com/konradjk