Vardict-java

Introduction

VarDictJava is a variant discovery program written in Java and Perl. It is a Java port of VarDict variant caller.

For more information, please check:

Docker hub: https://hub.docker.com/r/hydragenetics/vardict

Home page: https://github.com/AstraZeneca-NGS/VarDictJava

Versions

• 1.8.3

Commands

• vardict-java

• var2vcf_paired.pl

• var2vcf_valid.pl

• testsomatic.R

• teststrandbias.R

Module

You can load the modules by:

module load biocontainers
module load vardict-java

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 vardict-java on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vardict-java
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers vardict-java

AF_THR="0.01" # minimum allele frequency
vardict-java -G genome.fasta \
    -f $AF_THR -N genome \
    -b input.bam \
    -c 1 -S 2 -E 3 -g 4 output.bed \
     |  teststrandbias.R \
     |  var2vcf_valid.pl \
     -N genome -E -f $AF_THR \
     > vars.vcf