CNVFinder

The CNVFinder algorithm has been designed to detect copy number variants (CNVs) in human population from large-insert clone DNA microarray covering the entire human genome in tiling path resolution (WGTP platform). CNVFinder has been implemented in Perl.

The Copy Number Variation (CNV) Project

The CNVFinder package contains 3 main elements:

the perl module CNVFinder.pm that is the core algorithm implementation
call_cnv.pl a script providing a simple command line interface to run the CNVFinder analysis
documentation : README + after installation man page foreach modules and scripts

[Genome Research Limited]

Download and documentation
Platforms and Installation
Contact
Publication

Download and documentation

Download CNVFinder from our FTP site
Download CNVFinder documentation from our FTP site
- After installation, manuals will be installed into the man directory (in path_to_your_installation_directory/man )
- You may also access the command line documentation with: perl path_to_your_installation_directory/bin/call_cnv.pl

Platforms and Installation

Platforms

CNVFinder has been developed and tested on UNIX platforms ( Mac OS X, Linux distributions ).

Perl is portable on Windows system, however CNVFinder has not been tested on Windows machine therefore there is no warranty about using the CNVFinder package on any Windows installation.

Installation

First you will need to have Perl install with version 5.8 minimum and install another module : Statistics::Descriptive that can be downloaded from the CPAN repository.

Then you will only need to use the Makefile provided in the CNVFinder package. Installation can be done in these few command lines in your favorite terminal:

tar xvfz CNVFinder_2.1.tar.gz
           cd CNVFinder/
           perl Makefile.PL PREFIX=/path_to_your_installation_directory/
           make
           make test
           make install

Do not forget to add to your PERL5LIB environment variables, the path to your CNVFinder installation directory:

export PERL5LIB=${PERL5LIB}:'/path_to_your_installation_directory/':'/path_to_your_installation_directory/share/perl/'

You should then be ready to use CNVFinder with the perl script call_cnv.pl (located into the bin directory in your installation directory).

To access command line documentation, simply type:

perl path_to_your_installation_directory/bin/call_cnv.pl

For a quick run test, you may type:

perl path_to_your_installation_directory/bin/call_cnv.pl -input_file path_to_your_installation_directory/bin/test.gff -analysis test -output_dir ./

This will run CNVFinder on the test.gff file with the default CNVFinder parameters.It will produce output as a GFF file into the current directory ( cf file test.gff.cnvs.gff )

Running CNVFinder.

Running CNVFinder on test data.

Contact

If you have any feedback or enquiries or encounter any problems with the CNVFinder software that are not addressed in the documentation, please contact ***aliastocome@sanger.ac.uk***.

Publication

Accurate and reliable high-throughput detection of copy number variation in the human genome.

Fiegler H, Redon R, Andrews D, Scott C, Andrews R, Carder C, Clark R, Dovey O, Ellis P, Feuk L, French L, Hunt P, Kalaitzopoulos D, Larkin J, Montgomery L, Perry GH, Plumb BW, Porter K, Rigby RE, Rigler D, Valsesia A, Langford C, Humphray SJ, Scherer SW, Lee C, Hurles ME and Carter NP

Genome research 2006;16;12;1566-74

PUBMED: 17122085; PMC: 1665640; DOI: 10.1101/gr.5630906