snpsift
Link to section 'Introduction' of 'snpsift' Introduction
Snpsift is a tool used to annotate genomic variants using databases, filters, and manipulates genomic annotated variants.
For more information, please check its website: https://biocontainers.pro/tools/snpsift and its home page on Github.
Link to section 'Versions' of 'snpsift' Versions
- 4.3.1t
Link to section 'Commands' of 'snpsift' Commands
- SnpSift
Link to section 'Module' of 'snpsift' Module
You can load the modules by:
module load biocontainers
module load snpsift
Link to section 'Example job' of 'snpsift' 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.
To run Snpsift on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=snpsift
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snpsift
SnpSift annotate -id dbSnp132.vcf \
variants.vcf > variants_annotated.vcf