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FREEC is a tool for the detection of copy-number changes and allelic imbalances using deep-sequencing data.

FREEC is a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data.

FREEC is available as a module on Apocrita.


To run the default installed version of FREEC, simply load the freec module:

$ module load freec
$ freec


    freec -conf <config file>

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load freec

freec -conf config_ctrl.txt