Breakpointer protocols

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Breakpointer specifications

Information


Unique identifier OMICS_00308
Name Breakpointer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The file or files containing alignments of single-end reads against a reference genome.
Input format BAM
Output data The predicted regions containing potential breakpoints of SVs.
Output format GFF
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Ruping Sun <>

Publication for Breakpointer

Breakpointer in pipeline

2017
PMCID: 5605365
PMID: 28865746
DOI: 10.1016/j.ebiom.2017.08.015

[…] with the unifiedgenotyper algorithm and annotated using an in-house program called bgicgannotation. structural variations were detected in parallel by two individual programs, batcnv and breakpointer (see fig. s4 b in the supplementary appendix). batcnv was based on a hidden markov model (hmm) algorithm and was used to detect large gene deletions and duplications by analyzing changes […]


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Breakpointer in publications

 (8)
PMCID: 5605365
PMID: 28865746
DOI: 10.1016/j.ebiom.2017.08.015

[…] with the unifiedgenotyper algorithm and annotated using an in-house program called bgicgannotation. structural variations were detected in parallel by two individual programs, batcnv and breakpointer (see fig. s4 b in the supplementary appendix). batcnv was based on a hidden markov model (hmm) algorithm and was used to detect large gene deletions and duplications by analyzing changes […]

PMCID: 5446134
PMID: 28552950
DOI: 10.1371/journal.pone.0178322

[…] genomics viewer (igv, http://www.broadinstitute.org/igv/). the scnas across the entire genome were then analyzed by gistic 2.0 [, ]., rearrangement detection was performed using dranger and breakpointer algorithms [, ], and visualized using the circos program (http://mkweb.bcgsc.ca/circos) []. however, exome sequencing is limited in power to detect rearrangements and few were detected., […]

PMCID: 4767593
PMID: 26829750
DOI: 10.1038/ng.3502

[…] bwa aln. reads from primgrafts that align to the mouse genome (mm10) with maximal editing distance of 3bp (based on bwa alignment) were filtered out. rearrangements were called with dranger and breakpointer,. due to the lack of matching normal controls, we could not use the default germline filtering. instead we have filtered against a panel of 100 non-matched normals, defining […]

PMCID: 4767685
PMID: 26829751
DOI: 10.1038/ng.3500

[…] mutect and indellocator, and visual inspection in igv. mutsig (version 2.0) was applied to detect significantly recurrent mutations. rearrangements and breakpoints were identified using dranger, breakpointer and visual inspection. all analyses were performed within firehose., following rna extraction (rneasy, qiagen), library construction was performed using a non-strand specific illumunia […]

PMCID: 4686820
PMID: 26638776
DOI: 10.1038/ncomms9866

[…] structural instability in the 30 clls genomes (see for patient characteristics), we first analysed rearrangements, and identified a total of 92 events using the dranger algorithm followed by breakpointer. this result corresponds to a median of 2.5 (range 0–15) rearrangements per genome, significantly fewer than most other cancers (), underscoring the relative stability of these cll […]


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Breakpointer institution(s)
Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
Breakpointer funding source(s)
Supported by Max Planck Society.

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