Overview
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.
The download package includes the executable file named 'breakdancer_max' in cpp folder, but you can also make a binary file by yourself.
Please read our paper for detailed algorithmic description.
New Version (BreakDancer-1.1_20100719) Feature
The main difference between this version and the previous version (BreakDancer-1.0_20100624) is that this one computes the copy number for each bam file and add them as the extra columns if any applied. If not, the extra columns give you 'NA'.
Another change is that now the SV calls only output the SV score greater than the option '-y', by default it is 30. Please change it according to your application.
Also, two more options were added: -a to print out copy number by library rather than bam file (by default on); -h to print out Allele Frequency column (by default off). Please contact us if you want to know more about Allele Frequency, which currently is only applicable to DEL type.
The copy number feature was only implemented in cpp but not perl. So there is no corresponding perl BreakDancerMax file in the perl directory. If you do not need the copy number feature and would like to do BreakDancerMax by perl, please download the previous version: BreakDancer-1.0_20100624.
Perl and Cpp, which one to choose?
If you need to compute the copy number along with detecting SVs, please use cpp version, since the perl version does not have this feature. On another hand, Cpp version of BreakDancerMax definitely has a time advantage (save around 90% time) over the perl version. However, while perl version can deal with both BAM and MAQ data, cpp version currently can only do BAM. There are also some options that cpp cannot do. If you need these options, please use the perl version. For the details of the missing options, please click on morecpp. The link is also on the left bar underneath 'Usage'.
How to install?
To install BreakDancer, first, download the package, which includes both the perl and cpp version. Please click here: 'Perl/Cpp Full Version', or underneath 'Code Download' on the left bar there is the link.
You need extra package to run BreakDancer, and they are different for perl and cpp version. Please click 'More about Perl Version' or 'More about Cpp Version' to see in details what environment or libraries are needed besides the code downloaded. You can find the links on the left bar under 'Usage'.
How to run?
Before running the cpp code, please name the executable file to be breakdancer_max (the current one is already named 'breakdancer_max'). We will give examples in other pages by the name 'breakdancer_max'. Then please click 'BreakDancer Pipeline' to see in details what environment or libraries are needed besides the code downloaded. For your convenient, the link is also on the left bar underneath 'Usage'.
How to cite?
Please cite the paper in the following link if you use this tool or any related. We appreciate that.
http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html