Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

Deep Whole-Genome Sequencing of 100 Southeast Asian Malays

(2013) Lai-Ping Wong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Whole-genome sequence–based analysis of high-density lipoprotein cholesterol

(2013) Alanna C Morrison et al.   NATURE GENETICS

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants

(2012) T. S. Shah et al.   BIOINFORMATICS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

(2010) S. Q. Le et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE