Exome sequence read depth methods for identifying copy number changes

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

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

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

(2013) Yuhao Shi et al.   BIOINFORMATICS

Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing

(2013) Joep de Ligt et al.   HUMAN MUTATION

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

(2013) Alberto Magi et al.   GENOME BIOLOGY

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

(2012) Mingfu Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

A regression model for estimating DNA copy number applied to capture sequencing data

(2012) Guillem J. Rigaill et al.   BIOINFORMATICS

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

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo 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

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Estimation of Copy Number Alterations from Exome Sequencing Data

(2012) Rafael Valdés-Mas et al.   PLoS One

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

(2011) Jarupon Fah Sathirapongsasuti 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

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

Detection of structural variants and indels within exome data

(2011) Emre Karakoc et al.   NATURE METHODS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Copy number variants in pharmacogenetic genes

(2011) Yijing He et al.   TRENDS IN MOLECULAR MEDICINE

13q deletion anatomy and disease progression in patients with chronic lymphocytic leukemia

(2010) H Parker et al.   LEUKEMIA

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Population-genetic nature of copy number variations in the human genome

(2009) Mamoru Kato et al.   HUMAN MOLECULAR GENETICS

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

Integrated detection and population-genetic analysis of SNPs and copy number variation

(2008) Steven A McCarroll et al.   NATURE GENETICS

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

(2008) Derek Y Chiang et al.   NATURE METHODS