Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Phasing of Many Thousands of Genotyped Samples

(2012) Amy L. Williams et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human Genetic Individuality

(2012) Maynard V. Olson   Annual Review of Genomics and Human Genetics

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

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

(2012)   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

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

(2012) Bryan Howie et al.   NATURE GENETICS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Limitations of the Human Reference Genome for Personalized Genomics

(2012) Jeffrey A. Rosenfeld et al.   PLoS One

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

(2012) Gholson J Lyon et al.   Genome Medicine

Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism

(2012) Maria H. Chahrour et al.   PLoS Genetics

A Fast, Powerful Method for Detecting Identity by Descent

(2011) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency

(2011) Alan F. Rope et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process

(2011) Verena Heinrich et al.   NUCLEIC ACIDS RESEARCH

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

Genotype Imputation with Thousands of Genomes

(2011) Bryan Howie et al.   G3-Genes Genomes Genetics

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

(2011) Frederick E. Dewey et al.   PLoS Genetics

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

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

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS