ensembl-vep.rst

Ensembl-vep

Introduction ~~~~~~~~ Ensembl-vep(Ensembl Variant Effect Predictor) predicts the functional effects of genomic variants.

For more information, please check:
Docker hub: https://hub.docker.com/r/ensemblorg/ensembl-vep
Home page: https://github.com/Ensembl/ensembl-vep

Versions

• 106.1
• 107.0
• 108.2

Commands ~~~~~~~ - vep - haplo - variant_recoder

Module

You can load the modules by:

module load biocontainers
module load ensembl-vep

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run ensembl-vep on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ensembl-vep
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers ensembl-vep

haplo -i bos_taurus_UMD3.1.vcf -o out.txt