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

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

Authors

Trevor Paterson

Martin Graham

Andy Law



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
Electronic 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

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VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees (1.1 Mb)
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Publisher Licence URL
http://creativecommons.org/licenses/by/2.0/

Copyright Statement
© 2012 Paterson et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.







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