Snpeff

Introduction

Snpeff is an open source tool that annotates variants and predicts their effects on genes by using an interval forest approach.

For more information, please check its website: https://biocontainers.pro/tools/snpeff and its home page on Github.

Versions

• 5.1d

• 5.1

Commands

• snpEff

Module

You can load the modules by:

module load biocontainers
module load snpeff

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.

Note

By default, snpEff only uses 1gb of memory. To allocate larger memory, add -Xmx flag in your command.:

snpeff -Xmx10g ## To allocate 10gb of memory.

To run Snpeff on our clusters:

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

module --force purge
ml biocontainers snpeff

snpEff GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf