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
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