Software: Snpeff
Description
Snpeff is an open source tool that annotates variants and predicts their effects on genes by using an interval forest approach.
Available Versions
| Unspecified: | 5.1 5.1d |
|---|
For more information, please check its website: https://biocontainers.pro/tools/snpeff and its home page on Github.
Commands
- snpEff
Module
You can load the modules by:
module load biocontainers
module load snpeff
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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