Evaluation of somatic copy number estimation tools for whole-exome sequencing data

Identification of copy number variants from exome sequence data

(2014) Pubudu Samarakoon et al.   BMC GENOMICS

Inferring copy number and genotype in tumour exome data

(2014) Kaushalya C Amarasinghe et al.   BMC GENOMICS

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

(2014) A. Alkodsi et al.   BRIEFINGS IN BIOINFORMATICS

Exome sequence read depth methods for identifying copy number changes

(2014) L. Kadalayil et al.   BRIEFINGS IN BIOINFORMATICS

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

(2014) Caleb F. Davis et al.   CANCER CELL

An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data

(2014) Renjie Tan et al.   HUMAN MUTATION

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

CANOES: detecting rare copy number variants from whole exome sequencing data

(2014) Daniel Backenroth et al.   NUCLEIC ACIDS RESEARCH

FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

(2013) Yuhao Shi et al.   BIOINFORMATICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control

(2013) Yan Guo et al.   Biomed Research International

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis

(2012) L. J. M. Coin et al.   BIOINFORMATICS

CONTRA: copy number analysis for targeted resequencing

(2012) Jason Li et al.   BIOINFORMATICS

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm 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

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

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

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

(2011) Xutao Deng   BMC BIOINFORMATICS

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

(2011) Dalila Pinto et al.   NATURE BIOTECHNOLOGY

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

Modeling Read Counts for CNV Detection in Exome Sequencing Data

(2011) Michael I. Love et al.   Statistical Applications in Genetics and Molecular Biology

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

(2010) A. McKenna et al.   GENOME RESEARCH

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The 50th anniversary of the discovery of trisomy 21: The past, present, and future of research and treatment of Down syndrome

(2009) André Mégarbané et al.   GENETICS IN MEDICINE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Copy number variations and cancer

(2009) Adam Shlien et al.   Genome Medicine

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms

(2008) W. Lai et al.   BIOINFORMATICS