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BreakDancer specifications


Unique identifier OMICS_00307
Name BreakDancer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Alignment files
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Ken Chen

Publication for BreakDancer

BreakDancer citations


Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] med against the human reference sequence GRCh37/Hg19. Quality control (QC), variant annotation, deduplication and metrics were generated for each sample. Manta ( and Breakdancer ( were used for the detection of structural variants. […]


A genome wide survey of mutations in the Jurkat cell line

BMC Genomics
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] uses a certain type of sequence information to identify specific categories of variants. Our variant caller suite consisted of four distinct tools and algorithms: The Genome Analysis Toolkit, Pindel, BreakDancer, and CNVnator [–].The Genome Analysis Toolkit (GATK) from the Broad Institute uses De Bruijn graph-based models to identify single-nucleotide substitutions and small insertions and deletio […]


Novel sequences, structural variations and gene presence variations of Asian cultivated rice

Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] resent the rice SV data obtained by calling against the Nipponbare reference genome using novoBreak because it had the lowest false positive rate when compared with results from several tools such as BreakDancer and Delly. This SV data set contains a total number of 93,683 SVs (deletions, inversions and duplications of >100 bps and <1 Mbps, and translocations), or an average of 12,178 SVs per geno […]


The genetic architecture of floral traits in the woody plant Prunus mume

Nat Commun
PMCID: 5923208
PMID: 29703940
DOI: 10.1038/s41467-018-04093-z

[…] 3.0). We further filtered SNPs with more than 10% samples with missing genotypes, or deviated from Hardy-Weinberg principle in some downstream analysis. Structural variants (SV) were identified using BreakDancer, which cataloged deletions, insertions, inversions, and intra-chromosomal translocations. […]


Clinically actionable mutation profiles in patients with cancer identified by whole genome sequencing

PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] h B-allele frequency (BAF) outputs, were analyzed and events flagged and visualized using Nexus Discovery Edition 7.5 (BioDiscovery, Inc., El Segundo, CA).Translocation events were investigated using BreakDancer (v1.4.5). Analysis was limited to a set of cancer-specific genes, as previously defined ().Presence of HPV was determined by alignment of tumor sample reads using bwa (). HPV was confirmed […]


Resistance promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient

PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] sample required us to run copyCat in tumor-only mode, followed by manual review to differentiate somatic from germline copy-number events.Putative structural variants were detected using the union of BreakDancer 1.4.5 () filtered by novo-realign and tigra-sv, and squaredancer 0.1 ( […]


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BreakDancer institution(s)
The Genome Center, Washington University School of Medicine, St Louis, MO, USA

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