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.