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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.

Versions

  • 0.4.1

Commands ~~~~~~~ - cnvnator - cnvnator2VCF.pl - plotbaf.py - plotcircular.py - plotrdbaf.py - pytools.py

Module

You can load the modules by:

module load biocontainers
module load cnvnator

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 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