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Copy number variation detection software tools | Whole-exome sequencing data analysis

High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases. Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from…
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XHMM
Desktop

XHMM eXome-Hidden Markov Model

Extracts copy-number signal from noisy read depth by leveraging the large-scale…

Extracts copy-number signal from noisy read depth by leveraging the large-scale nature of sequencing projects to discern patterns of read-depth biases. XHMM is a statistical toolset that normalizes…

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SPLITREAD
Desktop

SPLITREAD

A method for detecting INDELs (small insertions and deletion with size less…

A method for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions deletions that are within the coding regions from the exome sequencing data.

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EXCAVATOR
Desktop

EXCAVATOR

A read count based tool that exploits all the reads produced by whole-exome…

A read count based tool that exploits all the reads produced by whole-exome sequencing (WES) experiments to detect copy Number Variants (CNVs) with a genome-wide resolution. EXCAVATOR2 enhances the…

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CoNIFER
Desktop

CoNIFER Copy Number Inference From Exome Reads

Uses exome sequencing data to find copy number variants (CNVs) and genotype the…

Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.

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CANOES
Desktop

CANOES Copy number variants with an Arbitrary Number Of Exome Samples

An algorithm for the detection of rare copy number variants from exome…

An algorithm for the detection of rare copy number variants from exome sequencing data. CANOES uses the negative binomial distribution. The method was applied to a family-based exome sequencing…

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CONTRA
Desktop

CONTRA

A tool for copy number variation (CNV) detection for targeted resequencing data…

A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

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ExomeCNV
Desktop

ExomeCNV

A statistical method to detect CNV and LOH using depth-of-coverage and B-allele…

A statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies from mapped short sequence reads in exome sequencing data. We apply ExomeCNV to a cancer exome resequencing…

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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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CODEX
Desktop

CODEX COpy number Detection by EXome sequencing

Provides a normalization and copy number variations (CNV) calling procedure for…

Provides a normalization and copy number variations (CNV) calling procedure for whole exome sequencing (WES) data. CODEX provides a R package for improving sensibility and specificity in detecting…

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cnvCapSeq
Desktop

cnvCapSeq

A method for accurate and sensitive CNV discovery and genotyping in long-range…

A method for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing.

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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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exomeCopy
Desktop

exomeCopy

A package for the detection of copy number variants (CNV) from exome sequencing…

A package for the detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. exomeCopy implements a hidden Markov model which uses positional covariates, such…

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FishingCNV
Desktop

FishingCNV

A software tool developed at McGill University, is a tool for comprehensive…

A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.

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DeAnnCNV
Web

DeAnnCNV Detection and Annotation of Copy Number Variations from WES data

An online tool designed for precise detection and annotation of copy number…

An online tool designed for precise detection and annotation of copy number variations (CNVs) from whole-exome sequencing (WES) data. Upon submitting the file generated from WES data by an in-house…

AS-GENSENG
Desktop

AS-GENSENG

Incorporates allele-specific read counts in CNV detection and estimates…

Incorporates allele-specific read counts in CNV detection and estimates accurate allele-specific copy number (ASCN) using either WGS or WES data. AS-GENSENG not only predicts ASCN calls but also…

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CKAT
Desktop

CKAT CNV Kernel Association Test

A copy number variant (CNV) kernel association test. CKAT is a real dataset…

A copy number variant (CNV) kernel association test. CKAT is a real dataset able to examine the association between CNV and disease as autism spectrum disorders (ASD) which demonstrates the potential…

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CLAMMS
Desktop

CLAMMS Copy number estimation using Lattice-Aligned Mixture Models

An algorithm for calling copy number variants (CNVs) from exome sequencing read…

An algorithm for calling copy number variants (CNVs) from exome sequencing read depths. CLAMMS is suitable for calling CNVs across the whole allele frequency spectrum, not just rare CNVs. Previous…

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cnvOffSeq
Desktop

cnvOffSeq

A normalization framework for off-target read depth that is based on local…

A normalization framework for off-target read depth that is based on local adaptive singular value decomposition (SVD). This method is designed to address the heterogeneity of the underlying data and…

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SLMSuite
Desktop

SLMSuite Shifting Level Model Suite

Permits to segment with high accuracy genomic profiles. SLMSuite is based on…

Permits to segment with high accuracy genomic profiles. SLMSuite is based on shifting level models (SLM) and heterogeneous shifting levels model (HSLM). It is specialized for microarray and…

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MEM pipeline
Desktop

MEM pipeline Mendelian Error Method pipeline

Identifies and validates deletion structural variation (SV) in trios with whole…

Identifies and validates deletion structural variation (SV) in trios with whole exome (WES) and whole genome sequencing (WGS) data. MEM pipeline is based on the principle that the presence of a…

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KaryoScan
Desktop

KaryoScan

Allows detection of chromosomal anomalies. KaryoScan consists in a scalable…

Allows detection of chromosomal anomalies. KaryoScan consists in a scalable normalization strategies for high-resolution detection of exonic copy-number variants (CNVs). This method proceeds to a…

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ERDS-pe
Desktop
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Anaconda
Desktop
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iCNV
Desktop

iCNV integrated Copy Number Variation caller

Allows copy number variation (CNV) detection. iCNV can be applied in whole…

Allows copy number variation (CNV) detection. iCNV can be applied in whole exome sequencing (WES) only, whole genome sequencing (WGS) only, single-nucleotide polymorphism (SNP) array only, or any…

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HMZDelFinder
Desktop

HMZDelFinder

Uses whole exome sequencing (WES) data to identify rare and intragenic…

Uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions. HMZDelFinder is an algorithm that enables evaluation of the distribution of 4866…

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ExomeDepth
Desktop

ExomeDepth

Calls copy number variants (CNVs) from targeted sequence data, typically exome…

Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. ExomeDepth was developed as a…

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CEQer
Desktop

CEQer Comparative Exome Quantification analyzer

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing…

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.

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PatternCNV
Desktop

PatternCNV

A versatile tool for detecting copy number changes from exome sequencing data.

A versatile tool for detecting copy number changes from exome sequencing data.

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VEGAWES
Desktop

VEGAWES

An R package for accurate and robust detection of copy number variations on WES…

An R package for accurate and robust detection of copy number variations on WES data. VEGAWES is an extension to a variational based segmentation algorithm, VEGA: Variational estimator for genomic…

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CONDEX
Desktop

CONDEX

Detects and calls rare copy number variants (CNVs) from exome sequencing data.…

Detects and calls rare copy number variants (CNVs) from exome sequencing data. CONDEX is a Hidden Markov Model (HMM) based method that uses depth information from the sequence to determine the…

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ExoCNVTest
Desktop

ExoCNVTest

An exome sequencing analysis pipeline to identify disease-associated CNVs and…

An exome sequencing analysis pipeline to identify disease-associated CNVs and to generate absolute copy number genotypes at putatively associated loci. This method re-discovered the LCE3B_LCE3C CNV…

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oCS
Desktop

oCS optimalCaptureSegmentation

A regression approach enables to deal with regions that are completely deleted,…

A regression approach enables to deal with regions that are completely deleted, which are problematic for methods that use log-ratios.

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ExonDel
Desktop

ExonDel

A tool specially designed to detect homozygous exon deletions efficiently.…

A tool specially designed to detect homozygous exon deletions efficiently. ExonDel provides researchers with a powerful tool to mine for internal deletions that may contain novel biological findings.

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