Indel variant analysis of short-read sequencing data with Scalpel

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Systematic discovery of complex insertions and deletions in human cancers

(2015) Kai Ye et al.   NATURE MEDICINE

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection

(2015) Yue Jiang et al.   NUCLEIC ACIDS RESEARCH

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

(2015) Rendong Yang et al.   Genome Medicine

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

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

(2014) Andy Rimmer et al.   NATURE GENETICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN 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

De novo mutations in histone-modifying genes in congenital heart disease

(2013) Samir Zaidi et al.   NATURE

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

(2013) Richard M. Leggett et al.   PLoS One

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

lobSTR: A short tandem repeat profiler for personal genomes

(2012) Melissa Gymrek et al.   GENOME RESEARCH

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

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

(2012) Zamin Iqbal et al.   NATURE GENETICS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

(2012) Gareth Highnam et al.   NUCLEIC ACIDS RESEARCH

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Detection of structural variants and indels within exome data

(2011) Emre Karakoc et al.   NATURE METHODS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Small insertions and deletions (INDELs) in human genomes

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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

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

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice

(2009) S. Fukuoka et al.   SCIENCE

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE