Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

Detection of Somatic Copy Number Alterations in Cancer Using Targeted Exome Capture Sequencing

(2015) Robert J. Lonigro et al.   NEOPLASIA

RSVSim: an R/Bioconductor package for the simulation of structural variations

(2013) C. Bartenhagen et al.   BIOINFORMATICS

Correction: CoNVEX: copy number variation estimation in exome sequencing data using HMM

(2013) Kaushalya C Amarasinghe et al.   BMC BIOINFORMATICS

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

(2013) Junbo Duan et al.   PLoS One

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes

(2012) T.-M. Kim 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

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comparative analysis of algorithms for integration of copy number and expression data

(2012) Riku Louhimo et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

(2012) Neeraja M. Krishnan et al.   PLoS One

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overcoming bias and systematic errors in next generation sequencing data

(2011) Margaret A Taub et al.   Genome Medicine

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

(2010) Sergii Ivakhno et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

(2010) Tae-Min Kim et al.   BMC BIOINFORMATICS

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

(2010) Kristian Ovaska et al.   Genome Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions

(2009) C G Mullighan et al.   LEUKEMIA

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH