snpeff
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'snpeff' Versions
- 5.1d
- 5.1
Link to section 'Commands' of 'snpeff' Commands
- snpEff
Link to section 'Module' of 'snpeff' Module
You can load the modules by:
module load biocontainers
module load snpeff
Link to section 'Example job' of 'snpeff' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
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