Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

Characterizing genetic variants for clinical action

(2014) Erin M. Ramos et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

(2014) Brandi L Cantarel et al.   BMC BIOINFORMATICS

Performance comparison of four exome capture systems for deep sequencing

(2014) Chandra Sekhar Chilamakuri et al.   BMC GENOMICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

(2014) Ming Yi et al.   NUCLEIC ACIDS RESEARCH

Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma

(2014) William R. Jeck et al.   Pigment Cell & Melanoma Research

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

(2014) Jing Shang et al.   Biomed Research International

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

(2014) Catherine A Brownstein et al.   GENOME BIOLOGY

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

(2013) Come Raczy et al.   BIOINFORMATICS

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

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

(2013) Aakrosh Ratan et al.   PLoS One

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

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

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

From targets to targeted therapies and molecular profiling in non-small cell lung carcinoma

(2012) A. Thomas et al.   ANNALS OF ONCOLOGY

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Consensus Rules in Variant Detection from Next-Generation Sequencing Data

(2012) Peilin Jia et al.   PLoS One

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

(2012) T. D. Andrews et al.   Open Biology

Application of next-generation sequencing in clinical oncology to advance personalized treatment of cancer

(2012) Yan-Fang Guan et al.   Chinese Journal of Cancer

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

(2011) H. Li   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

(2011) Joke Reumers et al.   NATURE BIOTECHNOLOGY

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

A comparative analysis of exome capture

(2011) Jennifer S Parla et al.   GENOME BIOLOGY

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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS