Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations

Correcting for Sample Contamination in Genotype Calling of DNA Sequence Data

(2015) Matthew Flickinger et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth

(2015) Rajen J. Mody et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

(2015) Timothy D. O’Brien et al.   METHODS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

(2015) Zhifu Sun et al.   Epigenomics

Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers

(2015) Jin Sung Jang et al.   Scientific Reports

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

(2015) Adam Cornish et al.   Biomed Research International

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

RVboost: RNA-seq variants prioritization using a boosting method

(2014) Chen Wang et al.   BIOINFORMATICS

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers

(2014) Zhifu Sun et al.   BMC Medical Genomics

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

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

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection

(2012) J. A. Neuman et al.   BRIEFINGS IN BIOINFORMATICS

Two Sides of the Same Coin: EGFR Exon 19 Deletions and Insertions in Lung Cancer

(2012) K. Politi et al.   CLINICAL CANCER RESEARCH

The transcriptional landscape and mutational profile of lung adenocarcinoma

(2012) J.-S. Seo et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

(2011) Gregory R. Grant et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

EGFR exon 20 insertion mutations in non-small-cell lung cancer: preclinical data and clinical implications

(2011) Hiroyuki Yasuda et al.   LANCET ONCOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Epidermal growth factor receptor in relation to tumor development: EGFR gene and cancer

(2009) Tetsuya Mitsudomi et al.   FEBS Journal

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

(2009) Ben Langmead et al.   GENOME BIOLOGY