	Prediction of copy number alterations and structural variants using deep-sequencing data FREEC-SV HOWTOs: Install all components Run FREEC-SV Visualize in Circos Contact: Valentina Boeva: FREEC@curie.fr phone: +33.1.56.24.69.88 Distributions: FREEC and SVDetect are free software; you can redistribute it and/or modify it under the terms of the GNU General Public License and GNU Public License correspondingly as published by the Free Software Foundation (www.fsf.org). Installation: Download and install FREEC here Download and install SVDetect here Download scripts to combine the output of the two programs here Run FREEC-SV Type `perl crossFreecSVDetect.pl` in the command line to get the list of functions Translate FREEC's output into Bed or Circos formats To translate an output of FREEC to a Bed file (so to view it in the UCSC Genome Browser) or to the Circos format, use these scripts: freec2bed.pl and freec2circos.pl Last modified: Jul 14 2011

Prediction of copy number alterations and structural variants using deep-sequencing data

FREEC-SV HOWTOs:

Install all components
Run FREEC-SV
Visualize in Circos

Contact:

phone: +33.1.56.24.69.88

Distributions:

FREEC and SVDetect are free software; you can redistribute it and/or modify it under the terms of the GNU General Public License and GNU Public License correspondingly as published by the Free Software Foundation (www.fsf.org).

Installation:

Download and install FREEC here
Download and install SVDetect here
Download scripts to combine the output of the two programs here

Run FREEC-SV

Type perl crossFreecSVDetect.pl in the command line to get the list of functions

Translate FREEC's output into Bed or Circos formats

To translate an output of FREEC to a Bed file (so to view it in the UCSC Genome Browser) or to the Circos format, use these scripts: freec2bed.pl and freec2circos.pl

Last modified: Jul 14 2011