Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

The BreakDancer package provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Program breakdancer-max predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.

References:

• https://www.nature.com/articles/nmeth.1363

• http://gmt.genome.wustl.edu/packages/breakdancer/documentation.html

• Module Name: breakdancer(see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
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 breakdancer
[user@cn3144 ~]$ bam2cfg.pl bam_file1 bam_file2 %BreakdancerOptions% > config_file.cfg
[user@cn3144 ~]$ breakdancer-max config_file.cfg > file.ctx

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

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

#!/bin/bash
set -e
module load breakdancer
breakdancer-max config_file.cfg > file.ctx

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

cd dir1; breakdancer-max config_file.cfg > file.ctx
cd dir2; breakdancer-max config_file.cfg > file.ctx
cd dir3; breakdancer-max config_file.cfg > file.ctx

Submit this job using the swarm command.

swarm -f job.swarm --module breakdancer

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module	Loads the module for each subjob in the swarm