Brass

Introduction

Brass is used to analyze one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.

For more information, please check its website: https://quay.io/repository/wtsicgp/brass and its home page on Github.

Versions

• 6.3.4

Commands

• brass-assemble

• brass_bedpe2vcf.pl

• brass_foldback_reads.pl

• brass-group

• brassI_filter.pl

• brassI_np_in.pl

• brassI_pre_filter.pl

• brassI_prep_bam.pl

• brass.pl

Module

You can load the modules by:

module load biocontainers
module load brass

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 Brass on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=brass
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers brass

brass.pl -c 4 -o myout -t tumour.bam -n normal.bam