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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.

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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). -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)

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