一，介绍
BreakDancer包含两个互补的程序：BreakDancerMax和BreakDancerMini。
BreakDancerMax根据二代测序read比对时，出现的异常比对，预测插入，缺失，倒位，染色体间或染色体内易位等五种结构突变。
BreakDancerMini则侧重于检测small indel。新版本的breakdancer已经不在包含BreakDancerMini，作者推荐使用Pindel检测small indels (10-80 bp)。
项目地址：https://github.com/genome/breakdancer http://breakdancer.sourceforge.net/
二，安装
BreakDancer利用跨平台编译工具cmake进行编译,如果没有安装cmake，要先安装cmake
$ sudo apt-get install cmake
git clone BreakDancer项目到本地，–recursive要添加，因为添加这个参数之后，BreakDancer引用的其他模块才会一并克隆到本地。modules说明在.gitmodules文件中。
$ git clone --recursive https://github.com/genome/breakdancer.git
创建build文件夹，并进入
$ cd breakdancer
$ mkdir build
$ cd build
执行cmake命令，指定编译发行版，并制定安装路径
$ cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
编译
$ make
$ sudo make install
有些教程提到要将samtools的路径添加到系统变量中，即在~/.profile或者~./bashrc中export PATH="${PATH}:/path/to/samtools。因为本人的服务器samtools本来就在环境变量中，所以没有设置，我在后续运行过程中发现breakdancer会调用samtools，所以请确保samtools在环境变量中。
在/path/tp/breakdancer/build/bin的目录下，会看到breakdancer-max。运行下试试，是不是正确输出了用法啦。
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
|
$ ./breakdancer-max
breakdancer-max version 1.4.5-unstable-66-4e44b43 (commit 4e44b43)
Usage: breakdancer-max
Options:
-o STRING operate on a single chromosome [all chromosome]
-s INT minimum length of a region [7]
-c INT cutoff in unit of standard deviation [3]
-m INT maximum SV size [1000000000]
-q INT minimum alternative mapping quality [35]
-r INT minimum number of read pairs required to establish a connection [2]
-x INT maximum threshold of haploid sequence coverage for regions to be ignored [1000]
-b INT buffer size for building connection [100]
-t only detect transchromosomal rearrangement, by default off
-d STRING prefix of fastq files that SV supporting reads will be saved by library
-g STRING dump SVs and supporting reads in BED format for GBrowse
-l analyze Illumina long insert (mate-pair) library
-a print out copy number and support reads per library rather than per bam, by default off
-h print out Allele Frequency column, by default off
-y INT output score filter [30]
|
