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CNVnator on Biowulf & Helix

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

Running on Helix

$ module load cnvnator
$ cd /data/$USER/dir
$ cnvnator
Not enough parameters.

CNVnator v0.3.1

Usage:
./cnvnator -root out.root  [-genome name] [-chrom 1 2 ...] -tree  file1.bam ...
./cnvnator -root out.root  [-genome name] [-chrom 1 2 ...] -merge file1.root ...
./cnvnator -root file.root [-genome name] [-chrom 1 2 ...] [-d dir] -his bin_size
./cnvnator -root file.root [-chrom 1 2 ...] -stat      bin_size
./cnvnator -root file.root                  -eval      bin_size
./cnvnator -root file.root [-chrom 1 2 ...] -partition bin_size [-ngc]
./cnvnator -root file.root [-chrom 1 2 ...] -call      bin_size [-ngc]
./cnvnator -root file.root -genotype bin_size [-ngc]
./cnvnator -root file.root -view     bin_size [-ngc]
./cnvnator -pe   file1.bam ... -qual val(20) -over val(0.8) [-f file]

Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19

Running a single batch job on Biowulf

1. Create a script file similar to the lines below.

#!/bin/bash

module load cnvnator
cd /data/$USER/dir
cnvnator command

2. Submit the script on biowulf:

$ sbatch jobscript

For more memory requirement (default 4gb), use --mem flag:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; cnvnator command
  cd /data/$USER/dir2; cnvnator command
  cd /data/$USER/dir3; cnvnator command
	[......]

Submit the swarm file:

  $ swarm -f swarmfile --module cnvnator

-f: specify the swarmfile name
--module: set environmental variables for each command line in the file

To allocate more memory, use -g flag:

  $ swarm -f swarmfile -g 10 --module cnvnator

-g: allocate more memory

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load cnvnator
cn999$ cd /data/$USER/dir
cn999$ cnvnator command

cn999$ exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem flag. For example

biowulf$ sinteractive --mem=10g

Documentation

https://github.com/abyzovlab/CNVnator