CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from targeted DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

• http://cnvkit.readthedocs.io/en/stable/quickstart.html

• Module Name: cnvkit (see the modules page for more information)
• Example files in /usr/local/apps/cnvkit/cnvkit-examples.
To test cnvkit with the example files:

  $ cp -r /usr/local/apps/cnvkit/cnvkit-examples /data/$USER
  $ cd /data/$USER/cnvkit-examples
  $ sinteractive --mem=5g
  $ module load cnvkit
  $ make
  

• Reference data in

  /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
  /fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa

• Sequencing-accessible regions files are under

/usr/local/apps/cnvkit/data
	  

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load cnvkit
[user@cn3144 ~]$ cnvkit.py autobin input.bam
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. cnvkit.sh). For example:

#!/bin/bash
set -e
module load cnvkit
cnvkit.py autobin input.bam

Submit this job using the Slurm sbatch command.

sbatch cnvkit.sh

Create a swarmfile (e.g. cnvkit.swarm). For example:

cd dir1; cnvkit.py autobin input.bam
cd dir2; cnvkit.py autobin input.bam
cd dir3; cnvkit.py autobin input.bam

Submit this job using the swarm command.

swarm -f cnvkit.swarm [-g #] --module TEMPLATE