Estimation of allele frequency and association mapping using next-generation sequencing data

Rare Variant Association Analysis Methods for Complex Traits

(2010) Jennifer Asimit et al.   Annual Review of Genetics

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

(2010) E. R. Martin et al.   BIOINFORMATICS

Design of association studies with pooled or un-pooled next-generation sequencing data

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

Accurate detection and genotyping of SNPs utilizing population sequencing data

(2010) V. Bansal 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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

(2010) Yingrui Li et al.   NATURE GENETICS

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

(2009) Kathryn E. Holt et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

(2009) Hua Bao et al.   BMC GENOMICS

Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects

(2009) M. Lynch   GENETICS

A probabilistic approach for SNP discovery in high-throughput human resequencing data

(2009) R. Hoberman et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Exome Sequencing of a Multigenerational Human Pedigree

(2009) Dale Hedges et al.   PLoS One

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

SNP frequency estimation using massively parallel sequencing of pooled DNA

(2008) Max Ingman et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics