cnvnator
Link to section 'Introduction' of 'cnvnator' Introduction
Cnvnator is a tool for discovery and characterization of copy number variation (CNV) in population genome sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/cnvnator and its home page on Github.
Link to section 'Versions' of 'cnvnator' Versions
- 0.4.1
Link to section 'Commands' of 'cnvnator' Commands
- cnvnator
- cnvnator2VCF.pl
- plotbaf.py
- plotcircular.py
- plotrdbaf.py
- pytools.py
Link to section 'Module' of 'cnvnator' Module
You can load the modules by:
module load biocontainers
module load cnvnator
Link to section 'Example job' of 'cnvnator' 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 Cnvnator on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cnvnator
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cnvnator
cnvnator -root file.root -tree file.bam -chrom $(seq 1 22) X Y
plotcircular.py file.root