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Somatic copy-number alteration detection software tools | Whole-exome sequencing data analysis

Somatic copy-number alterations (SCNAs) are an important type of structural variation affecting tumor pathogenesis. Accurate detection of genomic regions with SCNAs is crucial for cancer genomics as these regions contain likely drivers of cancer…
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VarScan
Desktop

VarScan

A platform-independent mutation caller for targeted, exome, and whole-genome…

A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan…

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Control-FREEC
Desktop

Control-FREEC

A tool for detection of copy-number changes and allelic imbalances (including…

A tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Control-FREEC automatically computes, normalizes, segments copy number and beta allele…

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VarDict
Desktop

VarDict

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict…

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict contains many features that are distinct from other variant callers, including linear performance to depth, intrinsic local…

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CNVkit
Desktop

CNVkit

A software tool for copy number detection that uses both the targeted reads and…

A software tool for copy number detection that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves…

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ADTEx
Desktop

ADTEx Aberration Detection in Tumour Exome

A tool for copy number variation (CNV) detection for whole-exome data from…

A tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. ADTEx uses ratio of tumour and matched normal average read depths at each exonic…

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Canvas
Desktop

Canvas

A tool for identification of copy number changes from diverse sequencing…

A tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched…

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CopywriteR
Desktop

CopywriteR

A tool for the detection of copy number aberrations from targeted sequencing.…

A tool for the detection of copy number aberrations from targeted sequencing. All currently available methods are based on exonic depth of coverage, and suffer from the problems that bait…

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CLOSE
Desktop

CLOSE Cna and LOh analysis with SEquencing data

A robust and efficient strategy for deriving global and allele-specific copy…

A robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. CLOSE is…

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MIRA
Desktop

MIRA Mutation Identification for RNA Alterations

Allows users to identify and characterize somatic mutation patterns in exons…

Allows users to identify and characterize somatic mutation patterns in exons and introns from coding and non-coding genes. MIRA can detect deep intronic mutations. It defines significantly mutated…

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WIFA-X
Desktop

WIFA-X

Allows identification of focal genomic aberrant regions in the whole-exome…

Allows identification of focal genomic aberrant regions in the whole-exome sequencing (WES) data from cancer cells. WIFA-X is a wavelet-based method that can be widely used for identifying cancer…

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CloneCNA
Desktop

CloneCNA

Addresses these issues and automatically detecting clonal and subclonal somatic…

Addresses these issues and automatically detecting clonal and subclonal somatic copy number alterations from heterogeneous tumor samples. CloneCNA fully explores the log ratio of read counts between…

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cnvCurator
Desktop

cnvCurator

A user-friendly tool with functions specifically designed to facilitate the…

A user-friendly tool with functions specifically designed to facilitate the process of interactively visualizing and editing somatic CNV calling results. Different from other general genomics…

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CoNCoS
Desktop

CoNCoS Copy Number estimation with Controlled Support

Increases the accuracy of copy number (CN) estimation in paired tumor/normal…

Increases the accuracy of copy number (CN) estimation in paired tumor/normal exome sequencing data sets by assessing and optimizing the support for a site-specific CN estimate. We show by simulations…

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