BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints. There are several stages the main component being:

• Collect read-pairs where both ends map but NOT marked as properly-paired.
• Perform grouping based on mapped locations
• Filter
• Run assembly
• Annotate with GRASS

• BRASS on GitHub

• Module Name: BRASS (see the modules page for more information)
• BRASS is part of the Cancer Genome Project and is closely related to the programs Ascat NGS and cgpBattenberg as well as the utilites VAGrENT and PCAP-core. All of these programs can be added to your path using the cancerit-wgs module. To get the most recent versions of all of these, use the cancerit-wgs/latest module version.
• Multithreaded. Note: the BRASS documentation recommends a max of 2 CPUs during the 'input' phase.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=20g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load BRASS

[user@cn3144 ~]$  brass.pl -c $SLURM_CPUS_PER_TASK -o myout -t tumour.bam -n normal.bam

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. BRASS.sh). For example:

#!/bin/bash
set -e
module load BRASS
brass.pl -c $SLURM_CPUS_PER_TASK -o myout -t tumour.bam -n normal.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=4] [--mem=20g] BRASS.sh

Create a swarmfile (e.g. BRASS.swarm). For example:

brass.pl -c $SLURM_CPUS_PER_TASK -o myout1 -t tumour1.bam -n normal.bam
brass.pl -c $SLURM_CPUS_PER_TASK -o myout2 -t tumour2.bam -n normal.bam
[...]

Submit this job using the swarm command.

swarm -f BRASS.swarm -g 15 -t 4 --module BRASS