A hybrid method for the imputation of genomic data in livestock populations

[1]  M. Calus,et al.  Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications. , 2014, Animal : an international journal of animal bioscience.

[2]  F. Schenkel,et al.  A new approach for efficient genotype imputation using information from relatives , 2014, BMC Genomics.

[3]  Ross M. Fraser,et al.  A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness , 2014, PLoS genetics.

[4]  J. Hickey,et al.  Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes , 2013, Genetics Selection Evolution.

[5]  Carl Nettelblad.  Breakdown of Methods for Phasing and Imputation in the Presence of Double Genotype Sharing , 2013, PloS one.

[6]  J. Marchini,et al.  Fast and accurate genotype imputation in genome-wide association studies through pre-phasing , 2012, Nature Genetics.

[7]  B. Kinghorn,et al.  A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation , 2012, Genetics Selection Evolution.

[8]  J. Hickey,et al.  Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods , 2012, G3: Genes | Genomes | Genetics.

[9]  José Crossa,et al.  Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs , 2012 .

[10]  O. Delaneau,et al.  A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.

[11]  Bruce Tier,et al.  A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes , 2011, Genetics Selection Evolution.

[12]  G. Abecasis,et al.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes , 2010, Genetic epidemiology.

[13]  Tom Druet,et al.  A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine Mapping , 2010, Genetics.

[14]  P. Donnelly,et al.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.

[15]  R. Fernando,et al.  Genomic Selection Using Low-Density Marker Panels , 2009, Genetics.

[16]  J. Grefenstette,et al.  High-resolution haplotype block structure in the cattle genome , 2009, BMC Genetics.

[17]  Sverker Holmgren,et al.  cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models , 2009, BICoB.

[18]  Gary K. Chen,et al.  Fast and flexible simulation of DNA sequence data. , 2008, Genome research.

[19]  M. Goddard.  The use of high density genotyping in animal health. , 2008, Developments in biologicals.

[20]  B. Browning,et al.  Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. , 2007, American journal of human genetics.

[21]  Paul Scheet,et al.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. , 2006, American journal of human genetics.

[22]  P. Donnelly,et al.  A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.

[23]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[24]  P M VanRaden,et al.  Genomic imputation and evaluation using high-density Holstein genotypes. , 2013, Journal of dairy science.

[25]  G. Abecasis,et al.  Merlin—rapid analysis of dense genetic maps using sparse gene flow trees , 2002, Nature Genetics.