Genotype imputation to increase sample size in pedigreed populations

John Hickey, M A Cleveland, C Maltecca, G Gorjanc, B Gredler, Andreas Kranis

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Abstract

Genotype imputation is a cost-effective way to increase the power of genomic selection or genome-wide association studies. While several genotype imputation algorithms are available, this chapter focuses on a heuristic algorithm, as implemented in the AlphaImpute software. This algorithm combines long-range phasing, haplotype library imputation, and segregation analysis and it is specifically designed to work with pedigreed populations.The chapter is organized in different sections. First the challenges related to genotype imputation in pedigreed populations are described, along with the specifics of the imputation algorithm used in AlphaImpute. In the second section, factors affecting the accuracy of genotype imputation using this algorithm are discussed. The different parameters that control AlphaImpute are detailed and examples of how to apply AlphaImpute are given.
Original languageEnglish
Title of host publicationGenome-Wide Association Studies and Genomic Prediction
EditorsCedric Gondro, Julius van der Werf, Ben Hayes
PublisherHumana Press
Pages395-410
ISBN (Print)978-1627034463
DOIs
Publication statusPublished - 30 Jun 2013

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume1019

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