[rat-forum] A new open source tool for structural variant discovery: RAPTR-SV

Bickhart, Derek Derek.Bickhart at ARS.USDA.GOV
Wed Feb 18 15:33:45 CST 2015

Hello everyone,

We are pleased to announce a public release of our new software, RAPTR-SV, for the discovery of Structural Variants (SV) from whole genome, paired-end sequence data. We have tested RAPTR-SV on two benchmark datasets, and it showed superior sensitivity in tandem duplication detection when compared to calls made by other, similar SV detection software -- specifically Lumpy-SV and Delly. Unlike other SV detection tools, RAPTR-SV was designed for use on non-model organism reference genomes as well as on high quality, finished reference assemblies. To better account for the uncertainty of assembly gaps -- which cause a large proportion of false-positive SV calls made by other software -- RAPTR-SV filters candidate SVs that span assembly gaps by default.

For a more detailed description of our algorithm and results, please see our publication in Bioinformatics:


RAPTR-SV is written in the Java programming language and it makes use of the JDK 1.8's new streaming paradigms in order to better utilize multiple processor cores for faster analysis. In order to view the source code for the program, download the latest release and view the documentation, please visit the github repository page:


Within the project's README, we provide a sample workflow and post- processing analysis steps that will result in genomic feature intersections of discovered SV regions. If you would like to provide feedback on the usage of this program or any bugs that you discover, please feel free to email me using my official email address:

derek.bickhart "at" ars.usda.gov

Thank you for your time,

Derek Bickhart
Research Geneticist
Animal Improvement and Genomics Laboratory
Building 005 rm 318
10300 Baltimore Avenue
Beltsville, MD 20705
Office: 301-504-8592

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