Control-FREEC.md

Protocol to detect copy number variation using Control-FREEC

Table of Contents

• About the tool
• Input
• Run Control-Freec
• Output
• Visualising CNVs in IGV

About the tool

Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH)

Input

Control-Freec has a very good manual that thoroughly explains options that can be set in config file.

Each sample needs an individual config file (start by editing config_WGS.txt).

For example see my example.config.txt for config for WGS mapped to Drosophila 6.12

Run Control-Freec

The main script is then called with the config file:

$ src/./freec -conf example.config.txt

Output

Files are written to directory specified in config file. See manual for description of output files.

Visualising CNVs in IGV

To create an IGV compatible track for each sample, run cf2gff.pl: