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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #310123

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: RAPTR-SV: a hybrid method for the detection of structural variants

Author
item Bickhart, Derek
item Hutchison, Jana - Edwards
item Xu, Lingyang
item Schnabel, Robert
item Taylor, Jeremy
item Reecy, James
item Schroeder, Steven - Steve
item Van Tassell, Curtis - Curt
item Sonstegard, Tad
item Liu, Ge - George

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/9/2015
Publication Date: 6/26/2015
Publication URL: http://handle.nal.usda.gov/10113/61483
Citation: Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-2090.

Interpretive Summary: Structural Variants, or large deletions and duplications of the genome of an individual, are likely linked to many diseases and productive traits in animals and humans but these variants are difficult to detect using modern DNA sequencing technologies. We have written a program, RAPTR-SV, that detects these variants from commonly used sequencing technologies without making a large number of false positive variant calls. Tests of RAPTR-SV on simulations and real data have revealed it to perform better than another program that uses a similar algorithm.

Technical Abstract: Motivation: Identification of Structural Variants (SV) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. Results: Simulations using RAPTR-SV and another software package that uses a similar algorithm for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a precision of 99.2%. When compared with calls made by other software on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified two-fold more duplications than a similar algorithm, while making approximately 85% fewer duplication predictions. Availability and Implementation: RAPTR-SV is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications. A compiled version of the software, instructions for usage and test results files are available on the GitHub repository page: https://github.com/njdbickhart/RAPTR-SV.