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
- 1.8.3
- vardict-java
- var2vcf_paired.pl
- var2vcf_valid.pl
- testsomatic.R
- teststrandbias.R
You can load the modules by:
module load biocontainers module load vardict-java
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