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

A comparative analysis of algorithms for somatic SNV detection in cancer

(2013) Nicola D. Roberts et al.   BIOINFORMATICS

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma

(2013) M. R. Green et al.   BLOOD

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

(2013) P. Jia et al.   GENOME RESEARCH

Accurately Identifying Low-Allelic Fraction Variants in Single Samples with Next-Generation Sequencing: Applications in Tumor Subclone Resolution

(2013) Lucy F. Stead et al.   HUMAN MUTATION

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

(2012) Andrew Roth et al.   BIOINFORMATICS

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

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

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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Consensus Rules in Variant Detection from Next-Generation Sequencing Data

(2012) Peilin Jia et al.   PLoS One

BRAF L597 Mutations in Melanoma Are Associated with Sensitivity to MEK Inhibitors

(2012) Kimberly Brown Dahlman et al.   Cancer Discovery

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

(2011) David E. Larson et al.   BIOINFORMATICS

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

(2011) Jiarui Ding et al.   BIOINFORMATICS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

(2011) Patrick Flaherty et al.   NUCLEIC ACIDS RESEARCH

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya 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 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