FREEC¶
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.
Usage¶
To run the default installed version of FREEC, simply load the
freec module:
$ module load freec
$ freec
Usage:
freec -conf <config file>
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load freec
freec -conf config_ctrl.txt