MOTIVATION: Identification of structural variants (SVs) 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 other, similar algorithms 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 Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified 2-fold more duplications than Delly, while making ∼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. CONTACT: derek.bickhart@ars.usda.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.
MOTIVATION: Identification of structural variants (SVs) 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 other, similar algorithms 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 Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified 2-fold more duplications than Delly, while making ∼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. CONTACT: derek.bickhart@ars.usda.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.
Authors: Jeremy F Taylor; Lynsey K Whitacre; Jesse L Hoff; Polyana C Tizioto; JaeWoo Kim; Jared E Decker; Robert D Schnabel Journal: Genet Sel Evol Date: 2016-08-17 Impact factor: 4.297
Authors: Zev N Kronenberg; Edward J Osborne; Kelsey R Cone; Brett J Kennedy; Eric T Domyan; Michael D Shapiro; Nels C Elde; Mark Yandell Journal: PLoS Comput Biol Date: 2015-12-01 Impact factor: 4.475
Authors: David L Oldeschulte; Yvette A Halley; Miranda L Wilson; Eric K Bhattarai; Wesley Brashear; Joshua Hill; Richard P Metz; Charles D Johnson; Dale Rollins; Markus J Peterson; Derek M Bickhart; Jared E Decker; John F Sewell; Christopher M Seabury Journal: G3 (Bethesda) Date: 2017-09-07 Impact factor: 3.154