CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

(2015) Marghoob Mohiyuddin et al.   BIOINFORMATICS

CODEX: a normalization and copy number variation detection method for whole exome sequencing

(2015) Yuchao Jiang et al.   NUCLEIC ACIDS RESEARCH

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data

(2014) Chen Wang et al.   BIOINFORMATICS

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data

(2014) Evangelos Bellos et al.   BIOINFORMATICS

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

(2014) Daniel Backenroth et al.   NUCLEIC ACIDS RESEARCH

Dissemination of scientific software with Galaxy ToolShed

(2014) Daniel Blankenberg et al.   GENOME BIOLOGY

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Recurrent BRAF kinase fusions in melanocytic tumors offer an opportunity for targeted therapy

(2013) Thomas Botton et al.   Pigment Cell & Melanoma Research

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

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

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

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

(2012) Jared J Gartner et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN 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

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

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation

(2011) Adam B. Olshen 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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

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

(2010) Valentina Boeva et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

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

(2009) S. Yoon et al.   GENOME RESEARCH

A fast and flexible method for the segmentation of aCGH data

(2008) E. Ben-Yaacov et al.   BIOINFORMATICS