Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip

Chris Schrooten; Romain Dassonneville; Vincent Ducrocq; Rasmus F Brøndum; Mogens S Lund; Jun Chen; Zengting Liu; Oscar González-Recio; Juan Pena; Tom Druet

doi:10.1186/1297-9686-46-10

Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip

Chris Schrooten, Romain Dassonneville, Vincent Ducrocq, Rasmus F Brøndum, Mogens S Lund, Jun Chen, Zengting Liu, Oscar González-Recio, Juan Pena, Tom Druet

Center for Quantitative Genetics and Genomics

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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Abstract

Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip. Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters. Imputation of genotypes was carried out from 50 000 (moderate-density) to 777 000 (high-density) SNPs (single nucleotide polymorphisms).

Original language	English
Journal	Genetics Selection Evolution
Volume	46
Issue	10
Pages (from-to)	1-9
Number of pages	9
ISSN	0999-193X
DOIs	https://doi.org/10.1186/1297-9686-46-10
Publication status	Published - 4 Feb 2014

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title = "Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip",

abstract = "Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip. Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters. Imputation of genotypes was carried out from 50 000 (moderate-density) to 777 000 (high-density) SNPs (single nucleotide polymorphisms).",

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language = "English",

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Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip. / Schrooten, Chris; Dassonneville, Romain; Ducrocq, Vincent et al.
In: Genetics Selection Evolution, Vol. 46, No. 10, 04.02.2014, p. 1-9.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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T1 - Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip

AU - Schrooten, Chris

AU - Dassonneville, Romain

AU - Ducrocq, Vincent

AU - Brøndum, Rasmus F

AU - Lund, Mogens S

AU - Chen, Jun

AU - Liu, Zengting

AU - González-Recio, Oscar

AU - Pena, Juan

AU - Druet, Tom

PY - 2014/2/4

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N2 - Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip. Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters. Imputation of genotypes was carried out from 50 000 (moderate-density) to 777 000 (high-density) SNPs (single nucleotide polymorphisms).

AB - Imputation of genotypes from low-density to higher density chips is a cost-effective method to obtain high-density genotypes for many animals, based on genotypes of only a relatively small subset of animals (reference population) on the high-density chip. Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters. Imputation of genotypes was carried out from 50 000 (moderate-density) to 777 000 (high-density) SNPs (single nucleotide polymorphisms).

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DO - 10.1186/1297-9686-46-10

M3 - Journal article

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SP - 1

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JO - Genetics Selection Evolution

JF - Genetics Selection Evolution

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ER -

Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip

Abstract

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