Software: Varscan
Description
Varscan is a tool used for variant detection in massively parallel sequencing data.
Available Versions
| Unspecified: | 2.4.2 2.4.4 |
|---|
For more information, please check its home page: http://varscan.sourceforge.net/index.html.
Commands
- VarScan.v2.4.4.jar
Module
You can load the modules by:
module load biocontainers
module load varscan
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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