VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees

Paterson, Trevor; Graham, Martin; Kennedy, Jessie; Law, Andy

Abstract

Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure.

Citation

Paterson, T., Graham, M., Kennedy, J., & Law, A. (2012). VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. BMC Bioinformatics, 13/8, https://doi.org/10.1186/1471-2105-13-S8-S5

• Journal Article Type: Article
• Publication Date: 2012
• Deposit Date: Apr 26, 2012
• Publicly Available Date: May 16, 2017
• Print ISSN: 1471-2105
• Publisher: BMC
• Peer Reviewed: Peer Reviewed
• Volume: 13/8
• DOI: https://doi.org/10.1186/1471-2105-13-S8-S5
• Keywords: Pedigree genotype datasets; genetic inheritance; VIPER; Visual Pedigree Explorer
• Public URL: http://researchrepository.napier.ac.uk/id/eprint/5227
• Publisher URL: http://dx.doi.org/10.1186/1471-2105-13-S8-S5
• Contract Date: May 16, 2017