Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis

(2014) H. C. Martin et al.   HUMAN MOLECULAR GENETICS

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

(2013) Come Raczy et al.   BIOINFORMATICS

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

From the periphery to centre stage: de novo single nucleotide variants play a key role in human genetic disease

(2013) Chee-Seng Ku et al.   JOURNAL OF MEDICAL GENETICS

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

(2013) Jason O'Rawe et al.   Genome Medicine

De Novo Pathogenic SCN8A Mutation Identified by Whole-Genome Sequencing of a Family Quartet Affected by Infantile Epileptic Encephalopathy and SUDEP

(2012) Krishna R. Veeramah et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

(2012) Jacob J. Michaelson et al.   CELL

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer

(2012) Elise Ruark 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

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies

(2011) Alistair T Pagnamenta et al.   JOURNAL OF HUMAN GENETICS

Transient hypermutability, chromothripsis and replication-based mechanisms in the generation of concurrent clustered mutations

(2011) Jian-Min Chen et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

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

(2011) Donald F Conrad et al.   NATURE GENETICS

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

(2011) Brian J O'Roak 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

A multi-site study using high-resolution HLA genotyping by next generation sequencing

(2011) C. L. Holcomb et al.   TISSUE ANTIGENS

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers 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

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

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

A Statistical Method for Predicting Classical HLA Alleles from SNP Data

(2008) Stephen Leslie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

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

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings

(2008) Mitch McVey et al.   TRENDS IN GENETICS

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH