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

Trevor Paterson, Martin Graham, Jessie Kennedy, Andy Law

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
Article numberS5
Pages (from-to)1-16
Number of pages16
JournalBMC Bioinformatics
Volume13
Issue numberSuppl 8
DOIs
Publication statusPublished - 2012
Event1st IEEE Symposium on Biological Data Visualization (BioVis 2011) - providence, United Kingdom
Duration: 23 Oct 201124 Oct 2011

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