UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

DJ Park; R Li; E Lau; P Georgeson; T Nguyen-Dumont; BJ Pope

Journal article

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

DJ Park, R Li, E Lau, P Georgeson, T Nguyen-Dumont, BJ Pope

BMC Bioinformatics | BMC | Published : 2016

DOI: 10.1186/s12859-016-1014-9

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Abstract

Background: Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent filtering of sequencing chemistry-induced errors by requiring reported variants to appear in both reads of overlapping pairs above certain thresholds of occurrence. ROVER was developed in tandem with Hi-Plex and has been used successfully to screen for genetic mutations in the breast cancer predisposition gene PALB2. ROVER is applied to MPS data in BAM format and, therefore, relies on sequence reads being mapped to a reference genome. In this paper, we describe an improvemen..

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University of Melbourne Researchers

Daniel Park Author

Peter Georgeson Author

Tu Nguyen Author

Bernard Pope Author

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Funding Acknowledgements

This work was supported by the Australian National Health and Medical Research Council (NHMRC) (APP1025879 and APP1029974), the National Institute of Health, USA (RO1CA155767), Cancer Council Victoria (APP1066612) and by a Victorian Life Sciences Computation Initiative (VLSCI) grant (number VR0182), on its Peak Computing Facility, an initiative of the Victorian Government. TN-D is a Susan G. Komen for the Cure Postdoctoral Fellow. RL was supported by the Undergraduate Research Opportunities Program (UROP), VLSCI and the Department of Pathology at The University of Melbourne. The authors would like to thank Benjamin Rubinstein from The University of Melbourne for his input into genotyping algorithms. All participants provided written informed consent for participation in the study. This study was approved by The University of Melbourne Human Research Ethics Committee.