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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.
To run this software interactively in a Linux environment, and is generally executed as follows :
module load breakdancer # create the configuration file needed by breakdancer using your # bam file. # NOTE: Be sure your BAM alignment file is sorted and has read # groups assigned (e.g., specified upfront in the mapping # using options to BWA or after the fact using PicardTools). bam2cfg -g -h your_mapping.bam > your_mapping.cfg# The -g and -h options above will give you insert size metrics # and distributions. You should make sure these have a single # peak, and not bimodal, or you will violate the assumptions of # the program. # Now you are ready to run the program. It is a good idea to # explicitly output the forward and reverse reads supporting the # called structural variants using the -d option, whose argument # will serve as the prefix to the two fastq files created. breakdancer_max -d SV_fastq_prefix your_mapping.cfg > out.ctx
Further documentation can be found here. It is helpful to refer to the general pipeline instructions provided by the author, and the output .ctx ASCII file format is well-described in the README document distributed with the software (e.g., /soft/breakdancer/1.1_2011_02_21/README)