CNVnator is a tool for CNV discovery and genotyping from depth of read mapping.

• https://www.ncbi.nlm.nih.gov/pubmed/21324876

• https://github.com/abyzovlab/CNVnator

• Module Name: cnvnator(see the modules page for more information)

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 cnvnator
[user@cn3144 ~]$ cnvnator -root Output.root -chrom 1 2
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load cnvnator
cnvnator -root Output.root -tree Input.bam

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

cd dir1; cnvnator -root Output.root -tree Input.bam
cd dir2; cnvnator -root Output.root -tree Input.bam
cd dir3; cnvnator -root Output.root -tree Input.bam

Submit this job using the swarm command.

swarm -f job.swarm --module cnvnator