Genotype imputation in the domestic dog

Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy

(2015) S. Bolormaa et al.   ANIMAL GENETICS

Accuracy of imputation using the most common sires as reference population in layer chickens

(2015) Marzieh Heidaritabar et al.   BMC GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications

(2014) M. P. L. Calus et al.   Animal

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy

(2014) Aniek C Bouwman et al.   BMC GENETICS

Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle

(2014) Rasmus Brøndum et al.   BMC GENOMICS

Improving accuracy of rare variant imputation with a two-step imputation approach

(2014) Eskil Kreiner-Møller et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Extent of linkage disequilibrium, consistency of gametic phase, and imputation accuracy within and across Canadian dairy breeds

(2014) S.G. Larmer et al.   JOURNAL OF DAIRY SCIENCE

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

(2014) Hans D Daetwyler et al.   NATURE GENETICS

Imputation and quality control steps for combining multiple genome-wide datasets

(2014) Shefali S. Verma et al.   Frontiers in Genetics

Extent of linkage disequilibrium in large-breed dogs: chromosomal and breed variation

(2013) Joshua A. Stern et al.   MAMMALIAN GENOME

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Genome-Wide Association Study Identifies a Novel Canine Glaucoma Locus

(2013) Saija J. Ahonen et al.   PLoS One

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Canine hip dysplasia is predictable by genotyping

(2011) G. Guo et al.   OSTEOARTHRITIS AND CARTILAGE

Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes

(2011) Li Li et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association identifies a deletion in the 3′ untranslated region of Striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy

(2010) Kathryn M. Meurs et al.   HUMAN GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex

(2010) Maria Wilbe et al.   NATURE GENETICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Localization of Canine Brachycephaly Using an Across Breed Mapping Approach

(2010) Danika Bannasch et al.   PLoS One

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Comprehensive Linkage Map of the Dog Genome

(2009) A. K. Wong et al.   GENETICS

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

(2008) F. C. F. Calboli et al.   GENETICS