BreakDancer-1.1, released under GPLv3, is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.

BreakDancerMax 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.

Installation Notes

Breakdancer requires sudo access due to installing the required perl modules.

Getting Breakdancer

sudo apt-get install subversion
svn co https://breakdancer.svn.sourceforge.net/svnroot/breakdancer
cd breakdancer

Getting Samtools-0.1.6

wget http://sourceforge.net/projects/samtools/files/samtools/0.1.6/samtools-0.1.6.tar.bz2
tar xjf samtools-0.1.6.tar.bz2
cd samtools-0.1.6
make

Should you receive an error when making and are on an Ubuntu/Linux system try changing the following line in Makefile:

samtools:lib $(AOBJS)
                $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam

to

samtools:lib $(AOBJS)
                $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam -lz

And running 'make' again.

It is now assumed that you are in the breakdancer directory, inside it you've placed a samtools-0.1.6 directory and have compiled the samtools directory

Alter Breakdancer's Makefile

Change the following line in Makefile:

all:
        g++ -g -Wall -O2 -I/Users/kchen/samtools/samtools-0.1.6 BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer-max -lm -lz -L/Users/kchen/samtools/samtools-0.1.6 -lbam

to

all:
        g++ -g -Wall -O2 -I samtools-0.1.6/ BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer_max -lm -L samtools-0.1.6/ -lbam -lz

Changing both the path of the -I and -L flag and also moving the -lz library flag after -lbam

Congrats! You've, hopefully, installed the CPP portion of Breakdancer. But there is also a Perl script that Breakdancer must run so we need to handle the prerequisites for that.

Prerequisites for bam2cfg.pl

Change the shebang/header in the bam2cfp.pl from:

#!/gsc/bin/perl

to

#!/usr/bin/env perl

Install the required perl modules.

sudo cpan install Math::CDF
sudo cpan install Statistics::Descriptive
sudo cpan install GD::Graph
sudo cpan install GD::Graph::histogram

Running Breakdancer

For sanity just update you PATH environmental variable to include looking into the breakdancer directory for bam2cfg.pl and breakdancer_max.

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