Control-freec

Introduction

Control-freec is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data.

For more information, please check its website: https://biocontainers.pro/tools/control-freec and its home page on Github.

Versions

11.6

Commands

freec

Module

You can load the modules by:

module load biocontainers
module load control-freec

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Control-freec on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=control-freec
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers control-freec

freec -conf config_chr19.txt