CNVkit

Introduction

CNVkit is a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

For more information, please check its website: https://biocontainers.pro/tools/cnvkit and its home page on Github.

Versions

0.9.9-py

Commands

cnvkit.py
cnv_annotate.py
cnv_expression_correlate.py
cnv_updater.py

Module

You can load the modules by:

module load biocontainers
module load cnvkit

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 CNVkit on our clusters:

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

module --force purge
ml biocontainers cnvkit

cnvkit.py batch *Tumor.bam --normal *Normal.bam \
                --targets my_baits.bed --fasta hg19.fasta \
                --access data/access-5kb-mappable.hg19.bed \
                --output-reference my_reference.cnn
                --output-dir example/