brass
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'brass' Versions
- 6.3.4
Link to section 'Commands' of 'brass' 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
Link to section 'Module' of 'brass' Module
You can load the modules by:
module load biocontainers
module load brass
Link to section 'Example job' of 'brass' Example job
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