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Bioinformatics. 2017 Oct 1;33(19):3121-3122. doi: 10.1093/bioinformatics/btx362.

BreakPoint Surveyor: a pipeline for structural variant visualization.

Author information

1
Oncology Division, Department of Medicine.
2
McDonnell Genome Institute.
3
Department of Pediatrics.
4
Department of Genetics.
5
Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA.
6
Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63108, USA.
7
Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA.

Abstract

Summary:

BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-sequencing expression into a single comprehensive figure.

Availability and implementation:

Source code and sample data freely available for download at https://github.com/ding-lab/BreakPointSurveyor, distributed under the GNU GPLv3 license, implemented in R, Python and BASH scripts, and supported on Unix/Linux/OS X operating systems.

Contact:

lding@wustl.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28582538
PMCID:
PMC5870665
[Available on 2018-10-01]
DOI:
10.1093/bioinformatics/btx362
[Indexed for MEDLINE]

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