Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

How do SNP ascertainment schemes and population demographics affect inferences about population history?

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Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Christopher C Chang et al.   GigaScience

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

(2014) Z. Edea et al.   Animal

Global diversity and genetic contributions of chicken populations from African, Asian and European regions

(2014) C. M. Lyimo et al.   ANIMAL GENETICS

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

(2014) Juan Herrero-Medrano et al.   BMC GENOMICS

Mapping signatures of positive selection in the genome of livestock

(2014) Saber Qanbari et al.   Livestock Science

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

(2014) Sithembile O. Makina et al.   Frontiers in Genetics

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

Development of a high density 600K SNP genotyping array for chicken

(2013) Andreas Kranis et al.   BMC GENOMICS

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

(2013) Nicolas Heslot et al.   PLoS One

Principal Components Analysis of Population Admixture

(2012) Jianzhong Ma et al.   PLoS One

A High Resolution Genome-Wide Scan for Significant Selective Sweeps: An Application to Pooled Sequence Data in Laying Chickens

(2012) Saber Qanbari et al.   PLoS One

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

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Genetic diversity and genealogical origins of domestic chicken

(2011) M. ELTANANY et al.   WORLDS POULTRY SCIENCE JOURNAL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic structure of a wide-spectrum chicken gene pool

(2009) Z. Granevitze et al.   ANIMAL GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

(2009) James W. Kijas et al.   PLoS One

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

(2009) David López Herráez et al.   PLoS One

Genome-wide patterns of population structure and admixture in West Africans and African Americans

(2009) K. Bryc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms

(2008) Ivan P. Gorlov et al.   AMERICAN JOURNAL OF HUMAN GENETICS

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

Population Substructure and Control Selection in Genome-Wide Association Studies

(2008) Kai Yu et al.   PLoS One

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

(2008) W. M. Muir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA