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

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

High quality SNP calling using Illumina data at shallow coverage

(2010) N. Malhis et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries

(2010) Michal Mokry et al.   NUCLEIC ACIDS RESEARCH

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

(2010) J. C. Roach et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

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

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

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

(2009) R. Hoberman et al.   GENOME RESEARCH

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Mapping Human Genetic Diversity in Asia

(2009) et al.   SCIENCE

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

(2009) R. Drmanac et al.   SCIENCE

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH