Research Output

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

  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.

  • Type:

    Article

  • Date:

    30 November 2011

  • Publication Status:

    Published

  • Publisher

    Biomed Central

  • DOI:

    10.1186/1471-2105-13-S8-S5

  • Library of Congress:

    QA76 Computer software

  • Dewey Decimal Classification:

    005 Computer programming, programs & data

Citation

Paterson, T., Graham, M., Kennedy, J. & Law, A. (2011). VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. BMC Bioinformatics. 13/8. doi:10.1186/1471-2105-13-S8-S5. ISSN 1471-2105

Authors

Keywords

Pedigree genotype datasets; genetic inheritance; VIPER; Visual Pedigree Explorer;

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