vardict-java
Link to section 'Introduction' of 'vardict-java' Introduction
VarDictJava is a variant discovery program written in Java and Perl. It is a Java port of VarDict variant caller.
Docker hub: https://hub.docker.com/r/hydragenetics/vardict
Home page: https://github.com/AstraZeneca-NGS/VarDictJava
Link to section 'Versions' of 'vardict-java' Versions
- 1.8.3
Link to section 'Commands' of 'vardict-java' Commands
- vardict-java
- var2vcf_paired.pl
- var2vcf_valid.pl
- testsomatic.R
- teststrandbias.R
Link to section 'Module' of 'vardict-java' Module
You can load the modules by:
module load biocontainers
module load vardict-java
Link to section 'Example job' of 'vardict-java' 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 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