Varscan
Introduction
Varscan
is a tool used for variant detection in massively parallel sequencing data.
For more information, please check its home page: http://varscan.sourceforge.net/index.html.
Versions
2.4.2
2.4.4
Commands
VarScan.v2.4.4.jar
Module
You can load the modules by:
module load biocontainers
module load varscan
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 Varscan on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=varscan
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers varscan