AbsCN-seq

• Description : AbsCN-seq is an R package for estimation of tumor purity, ploidy, and copy number variation (CNV) in next-generation sequencing data.

ABSOLUTE

• Description : ABSOLUTE is a tool for estimating tumor purity and cell ploidy by computing copy number variation (CNV) and multiplicity of mutations.

Accurity

• Description : Accurity is a software tool for inferring tumor cell ploidy, tumor purity, and absolute allelic copy numbers for somatic copy number alterations in whole-genome sequencing (WGS) data.

ACE

• Description : ACE is an R tool package for evaluating absolute copy number variation (CNV) and estimates tumor purity and ploidy. The algorithm uses low coverage whole genome sequencing (WGS) reads and obtains data segments from the QCDA pipeline, which puts the sequenced read into bins. ACE computes and fits the segment length by iteratively measuring error rates, using the root mean square error (RMSE) or mean absolute error (MAE). The Authors claim ACE to perform better than ABSOLUTE and ichorCNA algorithms.

ACNE

• Description : ACNE is a tool to estimate allele-specific copy numbers (CNs) in Affymetrix SNP array data. The ACNE algorithm uses the cross hybridization probe data. ACNE is a part of the Aroma project. See links below.

aCNViewer

• Description : aCNViewer is a tool for visualization of copy number variation (CNV) and loss of heterozygosity (LOH) in tumor samples. aCNViewer uses the Docker application. Requires: R, Python, Mode, Affymetrix power tools, Ascat, sequenza, and ggplot2.

ADMIRE

• Description : ADMIRE is a tool for identification repeated copy number variation (CNV). The ADMIRE algorithm identifies recurrent, multi-scale events, and uses multi-scale Gaussian smoothing. The ADMIRE algorithm does not require segmentation nor calling for the input dataset because it controls the false recovery analytically. The output of the algorithm is a single profile of significant events selected from the scales.

ADTEx

• Description : A tool for detection of copy number variation (CNV) in whole-genome exome data from paired or healthy tumor samples. The ADTex algorithm uses Hidden Markov Models (HMM) to predict CNV counts, genotypes, polyploidy, aneuploidy, cell contamination, and baseline shifts. The authors originally named ADTex to CoNVEX, but they changed the name because of the conflict with another tool.

Affy6CNV

• Description : Affy6CNV is a pipeline and a wrapper for the Birdsuite package to call copy number variation (CNV) from Affymetrix 6.0 genotyping array data.

AluScanCNV2

• Description : An R package AluScanCNV2 is based on the previously developed AluScanCNV tool. This tool is specifically designed for copy number variation (CNV) calling from next-generation sequencing (NGS) data and for germline CNV-based cancer risk prediction. It uses Geary-Hinkley transformation (GHT)-based comparison of the read-depth.

Anaconda (USTC)

• Description : A pipeline tool for detection and annotation of somatic copy number variation (CNV). The algorithm includes the following CNV detection methods: ExomeCNV, FREEC, ADTEx and EXCAVATOR.

AneuFinder

• Description : AneuFinder is an R package for copy number variation (CNV) detection, breakpoint detection, karyotype, and heterogeneity analysis between single cells.

aroma.affymetrix

• Description : aroma.affymetrix is an R package for the analysis of Affymetrix data to detect copy number variation (CNV). The aroma.affymetrix algorithm computes an unbiased reference signal from the test samples using publicly available reference sets in an attempt to eliminate an in-house reference.

BACOM

• Description : BACOM (Bayesian Analysis of COpy number Mixtures) is a package that contains a pipeline for copy number variation (CNV) analysis in heterogeneous cancer cell sample data. BACOM also estimates deletions and tissue contamination. See also links for BACOM2.0.
  Alternative name: bacomR (an R interface for BACOM Java version).

BACOM2.0

• Description : BACOM2.0 (Bayesian Analysis of COpy number Mixtures) is an improved version of BACOM (see links) package that contains a pipeline for copy number variation (CNV) analysis in heterogeneous cancer cell sample data. BACOM also estimates deletions and tissue contamination. The main improvement consists of an enhanced allele-specific normalization method.
  Alternative name: bacomR (an R interface for BACOM Java version).
  Note: BACOM2.0 requires original BACOM program (download) to read and process raw SNP array data (.CEL files). See links below.

Bamgineer

• Description : A tool to simulate haplotype-phased allele-specific copy number variation (CNV) into a Binary Alignment Mapping (BAM) and cancer CNVs in exome and targeted cell-free DNA sequencing data.

BubbleTree

• Description : BubbleTree is an R package for analysis of tumor samples in next generation sequencing (NGS) data. The BubbleTree algorithm can estimate cancer causing cell inpurity, ploidy, clonality, and allele-sepcific copy number variation (CNV). It displays the results in a graph format. The Authors claim that BubbleTree out performs THetA2, ABSOLUTE, AbsCN-seq and ASCAT tools.

CANOES

• Description : CANOES is a tool for detection of copy number variation (CNV) in whole-genome exome sequencing data. The CANOES algorithm uses the negative binomial distribution to model read counts and a regression-based method on user-selected reference samples.

CaSNP

• Description : CaSNP is a database for storing and quantitatively examining copy number variation (CNV) in data from SNP arrays. The CaSNP database contains 34 different cancer types from 104 studies. The database includes a heatmap visualization for estimated CNVs for each SNP marker site.

CCRET

• Description : A tool to detect copy number variation (CNV). The algorithm models the effects of CNV features in multiple categories..

CLImAT-HET

• Description : CLImAT-HET is a tool for the detection of subclonal copy number variation (CNV) and loss of heterozygosity in tumor samples. The CLImAT-HET algorithm uses whole-genome sequencing (WGS) data and a factorial hidden Markov model.

ClinTAD

• Description : A tool for interpretation of copy number variation (CNV) in the context of topologically associated domains (TADs).

CloneCNA

• Description : CloneCNA is a tool to detect copy number variation (CNV) in heterogeneous tumor samples in whole-genome exome sequencing data. The CloneCNA algorithm identifies clonal and subclonal CNVs by computing the log-ratio of the read counts of paired healthy samples and tumor B allele frequencies in germline at independent SNP locations.

cn.farms

• Description : cn.farms is an R package for copy number variation (CNV) analysis of the Affymetrix (250K-SNP6.0) array types. It uses snow and ff.

cn.mops

• Description : cn.mops (Copy Number estimation by a Mixture Of PoissonS) is an R package pipeline for analysis of copy number variation (CNV) in next-generation sequencing (NGS) data. The cn.mops pipeline contains a function for conversion of BAM files into read count matrices and genomic ranges. The algorithm uses Bayesian and Poisson statistics to model the depth coverage and filter out noise.

CnD

• Description : CnD is a tool for detection of copy number variation (CNV) in inbred mouse strains. Contact the webmaster or the Authors for availability.

CNOGpro

• Description : CNOGpro is an R package for detection and identification of copy number variation (CNV) specifically in prokaryotic whole-genome sequencing data. The tool uses Hidden Markov Model (HMM) and bootstrapping.

CNspector

• Description : CNspector is a web-based tool for clinical diagnosis and visualization of copy number variation (CNV) using next-generation sequencing (NGS) data.

CNV-RF

• Description : CNV-RF is a tool for detection of copy number variation (CNV) in next-generation sequencing (NGS) data. The algorithm is based on the random forest approach.

CNV-seq

• Description : CNV-seq is a tool for copy number variation (CNV) estimation. The algorithm uses a robust statistical method for the assessment of CNV.

CNValidator

• Description : CNValidator is a tool for evaluation of the correctness of somatic copy number calls. The CNValidator algorithm analyses the coherency of haplotypes taking several samples from a single individual.

CNVannotator

• Description : CNVannotator is a web-based tool for annotating copy number variation (CNV) in the human genome. The features include ENCODE regulatory elements, cytobands, segmental duplications, fragile genome sites, pseudogenes, promoters, enhancers, CpG islands, and methylation sites. CNVannotator permits users to apply various filters to reveal subgroups of CNVs, that for example, connected to tumor suppressor genes and oncogenes.

CNVcaller

• Description : CNVcaller is a tool for the detection of copy number variation (CNV) in large populations. Requirements: SAMtools 1.3 (using htslib 1.3), scikit-learn v0.19.0.

cnvCapSeq

• Description : cnvCapSeq is a tool to detect copy number variation (CNV) and to genotype using long-range targeted resequencing.

CNVD

• Description : CNVD (Copy Number Variation in Disease) is a web-based, manually curated database for copy number variation (CNV) in disease.

CNVeM

• Description : A tool to detect copy number variation (CNV). The algorithm uses expectation-maximization (EM) algorithm to estimate locations and the number of copies.

CNVer

• Description : A tool to detect copy number variation (CNV). CNVer algorithm uses paired-end, matepair, information together with the donor graph framework to adjust coverage for localized sequencing biases.

CNVfinder

• Description : CNVfinder is a tool to detect copy number variation in whole-genome exome sequencing data generated using amplicon-based enrichment technologies.

cnvGSA

• Description : cnvGSA is an R package designed for testing the gene-set rare variant burden in case-control studies of copy number variation (CNV).

cnvHap

• Description : cnvHap tool is for detection of copy number variation (CNV) and genotypes. The algorithm learns the chromosome-wide haplotype model of CNVs and cluster-based models of allele intensities and integrates data from from multiple sources. It can also predict copy number association. The Authors claim cnvHap to detect more genotypes than PennCNV and QuantiSNP. Available from the Author.

cnvHiTSeq

• Description : cnvHiTSeq is a tool to detect copy number variation (CNV) and genotyping population sequencing data. The cnvHiTSeq algorithm incorporates evidence from the read depth, read pair orientation, split reads, and uses a hidden Markov model to make an integrated analysis of the data from the separate sources.

CNVineta

• Description : CNVineta is an R tool to mine and visualize copy number variation (CNV) in case-control oligonucleotide array data, genotyped by single nucleotide polymorphism (SNP). The CNVineta algorithm is compatible with several current CNV prediction tools. It can also visualize log2 ratios and allele frequencies.

CNVinspector

• Description : A tool for evaluation of copy number variation (CNV). CNVinspector is a web-based tool and allows users to interactively analyse both single patients and cohorts and is optimized for Mozilla Firefox.

CNVkit

• Description : CNVkit is a tool for detection and visualization of copy number variation (CNV). The algorithm uses targeted and off-target sequence reads for the inference of CNV.

CNVnator

• Description : A tool for discovery and characterization of copy number variation (CNV) in population genome sequencing data. The tool is also well suited for personal genome analysis. The method is based on the mean-shift, Multiple-bandwidth partitioning, and GC correction.

cnvOffSeq

• Description : cnvOffSeq is specifically designed for the detection of intergenic copy number variation (CNV) using off-target exome sequencing data. The algorithm uses local adaptive singular value decomposition (SVD) to normalize off-target.

CNVPanelizer

• Description : A tool for classification of copy number variation (CNV) at the gene level. The algorithm uses a non-parametric bootstrap subsampling of references and a random forest like algorithm to associate the amplicons with the targeted genes.

CNVphaser

• Description : CNVphaser is a tool to infer alleles or haplotypes in copy number variable (CNV) genomic regions. The CNVphaser algorithm uses Partition-Ligation–Expectation-Maximization (PL-EM), and users may set three different initial value types. The algorithm can handle missing calls, any number of variant base types, and seed prior copies in the enumeration procedure of the EM algorithm. Note, an improved version, CNVphaserPro, is available. See links. (For noisy CNV data: MOCSphaser from the same research group).

CNVphaserPro

• Description : CNVphaser is a tool to infer alleles or haplotypes in copy number variable (CNV) genomic regions. The CNVphaser algorithm uses Partition-Ligation–Expectation-Maximization (PL-EM), and users may set three different initial value types. The algorithm can handle missing calls, any number of variant base types, and seed prior copies in the enumeration procedure of the EM algorithm. (For noisy CNV data: MOCSphaser from the same research group).

CNVrd2

• Description : CNVrd2 is a command-line tool for the detection of copy number variation (CNV). The algorithm uses a linear regression model and a Bayesian normal mixture model for estimating individual copy number counts.

CNVtest

• Description : An R tool for testing copy number variation (CNV) association based on log-ratio data of SNP arrays.

CNVtools

• Description : CNVtools is an R package designed for testing of copy number variation (CNV) data to facilitate association studies.

CNV_IFTV

• Description : CNV_IFTV is a tool for detection of copy number variation (CNV). The algorithm is specifically designed for short read data. It uses a novel 'isolation forest' algorithm.

CNV_SS

• Description : A tool to detect copy number variation (CNV). The algorithm uses the Gaussian convolution at various set scales and finds the locations of CNVs by analysis of a finger print map.

CN_Learn

• Description : CN_Learn is a tool for copy number variation (CNV) detection. The algorithm integrates multiple CNV detection algorithms and learns to identify CNVs based on validated CNVs.

CODEX2

• Description : CODEX2 is a tool for detecting copy number variation (CNV) in high-throughput sequencing data. The CODEX2 algorithm is well suited for studies with and without negative control samples and is sensitive enough to detect rare population frequencies.

CONDEL

• Description : CONDEL (CONsensus DELeteriousness) is a software tool to detect copy number variation (CNV) in single tumor sample sequencing data. The CONDEL algorithm uses a Bayesian method to infer CNV and zygosity, and it uses a unique statistics combined with a peel-off scheme for assessment of significances.

Contra

• Description : Contra is a tool to detect copy number variation (CNV) from targeted resequencing data. It reports gains and losses in respect to a normalized depth of coverage.

Control-FREEC

• Description : Control-FREEC is a tool for detection of copy number variation (CNV) and allelic imbalances (LOH) in deep-sequencing data. Control-FREEC algorithm normalizes CNV and beta allele frequencies whereafter it assigns CNVs and LOH. Control-FREEC can use mappability files generated by the GEM tool.
  Alternative name: FREEC.

conumee

• Description : conumee is a set of processing and plotting methods for making copy-number variation (CNV) analysis using Illumina 450k and EPIC methylation arrays.

CoNVaDING

• Description : A tool for indentification of copy number variation (CNV) specifically in next-generation sequencing (NGS) data. CoNVaDING algorithm contains quality control metrics and can be used for clinical diagnostics. Requires: samtools, Perl, and the Statistics::Normality package for perl.

CoNVaQ

• Description : A web-based tool for copy number variation (CNV) - based association studies. CoNVaQ has two models: 1. Fisher's exact test and 2. A novel query-based model matching regions to user-defined queries.

COPS (Bio-IT Centre)

• Description : COPS is a tool for detection of copy number variation (CNV) in paired-end sequencing data. The COPS algorithm requires data from both normal and disease samples.

CopyMap

• Description : CopyMap is a tool for detection of copy number variation (CNV) and allele frequencies in oligo-hybridization and CGH data. The CopyMap algorithm uses a time-dependent hidden Markov model (HMM) to consolidate data of copy number variants (CNVs) across various carriers.

DBS

• Description : DBS (Deviation Binary Segmentation) is a tool for segmenting copy number variable (CNV) genomic locations. The inspiration for the DBS algorithm originates from the segmentation method based on the circular binary segmentation method. It uses a point-by-point model calculation coupled with a binary search algorithm with heuristics derived from the Central Limit Theorem. DBS can measure the change-point amplitude of mean values of two neighboring segments at a breakpoint.

DeAnnCNV

• Description : DeAnnCNV (Detection and Annotation of Copy Number Variations) is a web-based tool to detect and annotate copy number variation (CNV) in whole genome exome sequencing. The algorithm is based on GPHMM tool (see links).

DEFOR

• Description : A tool for detection of somatic copy-number variation in tumor sample data. The DEFOR algorithm accounts for coverage, allele frequencies, and allows large-scale copy-number variation (CNV).

DNACopyNumber

• Description : DNACopyNumber is a tool for detection of copy number variation (CNV). The DNACopyNumber algorithm us based on penalized least squares regression and bootstrapping to estimate the statistical significance.

DupHMM

• Description : DupHMM is a tool for detection of copy number variation (CNV) of reads mapped to a reference genome. The DupHMM algorithm sections chromosomes into user specified window sizes and uses Poisson distribution to emit probabilities to a Hidden Markov Model (HMM) to model single copy and duplicated chromosomal regions.

Ensemble Variant Effect Predictor

• Description : Ensembl Variant Effect Predictor predicts the effects of single nucleotide polymorphism (SNPs), copy number variation (CNV), and indels on genes, transcripts, protein, and regulatory sequences.

EnsembleCNV

• Description : EnsembleCNV is a tool to detect and genotype copy number variation (CNV). It uses single nucleotide polymorphism (SNP) data. The algorithm eliminates batch effects on raw data, assembles CNV calls into regions by a heuristic algorithm, re-computes genotypes for each copy number variable region using an adjusted local likelihood model, computes refined CNV boundaries, and CNV genotypes with a confidence score.

ERDS

• Description : ERDS a tool for detection of copy number variants (CNVs) on human genomes in next-generation sequencing data. The approach is based on paired Hidden Markov models (PHMM) and on the expected distribution of read depth detected by heterozygous sites. ERDS is NOT a good choice for the analysis of exome data.
  The Author is no longer maintaining the package, but the source code is available.

EXCAVATOR

• Description : EXCAVATOR is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states.

EXCAVATOR2

• Description : EXCAVATOR2 is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR2 algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states. EXCAVATOR2 is an enchanced version of EXCAVATOR (see links).

ExCNVSS

• Description : ExCNVSS is a software tool to detect copy number variation (CNV) in whole-genome exome sequencing data. The ExCNVSS algorithm is based on an evaluation of the coverage and uses a scale-space filtering approach to resolve coverage biases.

ExomeCNV

• Description : ExomeCNV is a tool for detection of copy number variation (CNV) and loss of heterozygosity (LOH). The algorithm uses statistics of sequence coverage and B-allele frequencies for the estimation of CNV and LOH.

exomeCopy

• Description : exomeCopy R package is for detection of copy number variants (CNV) from exome and unpaired sample sequencing. The implementation is based on a hidden Markov model on background read depth and GC-content to normalize copy count.

ExomeDepth

• Description : A tool for calling copy number variation (CNV) from targeted exome sequencing data. ExomeDepth tool is specifically designed to address technical variability between the samples.

FACETS

• Description : FACETS is an analysis pipeline for analysis of allele-specific copy number for whole-genome and targeted sequencing data.

G-CNV

• Description : G-CNV is a GPU-based tool to prepare sequences for copy number variation (CNV) analysis. This tool filters and masks low-quality reads and nucleotides discard adapter sequences and duplicated reads map and resolve mapping ambiguities compute and normalize read-depth.
  Supported GPUs: CUDA enabled NVIDIA (kepler), cc 3.5.

Genovar

• Description : Genovar is a tool for detection of copy number variation (CNV). It can compare detected CNVs with variants in the Database of Genomic Variants ( DGV) to find out whether variants are novel or previously detected. Genovar can visualize genomic source data, e.g., aCGH and sequence alignment data.

GENSENG

• Description : GENSENG is a tool for detecting copy number variation (CNV). The algorithm uses a hidden Markov model and negative binomial regression for the identification of CNVs.

Ginkgo

• Description : A web-based tool for the analysis of single-cell copy-number variations (CNVs). It compiles copy number profiles from mapped reads and constructs phylogenetic trees of related cells.

GISTIC

• Description : GISTIC is a tool to identify genes targeted by somatic copy number variation (CNV). The GISTIC algorithm defines CNV boundaries by a user-defined confidence level.
  Alternative name: GISTIC2.

GPHMM

• Description : GPHMM (Global Parameter Hidden Markov Model) is a tool for identification of copy number variation (CNV) and loss of heterozygosity (LOH) in whole-genome single nucleotide (SNP) array data. The specific purpose of GPHMM is the analysis of tumor samples. The algorithm uses a hidden Markov model (HMM) to solve issues caused e.g., by a baseline shift of LRR signal, cell contamination, and genomic waves.

HadoopCNV

• Description : HadoopCNV is for detection of copy number variation (CNV) using 'Dynamic Programming Imputation' algorithm and based on Hadoop platform. The tool works on next-generation sequencing (NGS) data.

HD-CNV

• Description : HD-CNV is a tool for identifying copy number variant (CNV) sites of interest by comparing CNVs between different samples. The algorithm finds cliques in a graph and produces spread sheet data and UCSC Genome Browser track files.

HMZDelFinder

• Description : HMZDelFinder is a tool for detection of homozygous/hemizygous copy number variation (CNV) in data from Mendelian disease cohorts.

hsegHMM

• Description : hsegHMM is a software tool to analyze copy number variation (CNV). The hsegHMM algorithm uses a hidden Markov model (HMM) as the basis that includes hypersegmentation and an E-M method.

ichorCNA

• Description : ichorCNA is an R tool for estimation of tumor fractions in ultra-low pass whole genome sequencing (WGS) and prediction of large-scale copy number variation (CNV). The ichorCNA algorithm uses a hidden Markov model (HMM) for the probabilistic modeling and works in sequencing coverages down to 0.1X.

iCNV

• Description : A tool for detecting copy number variation (CNV) in various study designs: whole-genome exome sequencing, whole-genome sequencing, and single nucleotide polymorphism (SNP). iCNV (integrated CNV) algorithm the Hidden Markov Model (HMM) to do platform-specific normalization and to integrate sequencing data with SNP-array data.

iCopyDAV

• Description : A pipeline to detect, visualize, and edit copy number variation (CNV). iCopyDAV has the following m,odules: data pre-treatment, segmentation, variant calling, annotation and visualization. Requires: samtools, bedtools, openMPI, and the R packages: DNAcopy, ParDNAcopy, quantsmooth, GenomicAlignments, and rtracklayer. iCopyDAV is also available as a Docker image.

Ioncopy

• Description : Ioncopy is a tool for calling copy number variation (CNV) in targeted next-generation sequencing (NGS) data. The Ioncopy algorithm uses multiple testing to control FWER/FDR and estimate the significance of the variation.

JointSLM

• Description : JointSLM an R package for the detection of copy number variation (CNV). The algorithm analyses coverage data simultaneously within multiple samples.

LRS

• Description : A tool for selecting a likelihood ratio based on SNP Chip LogR data for copy number variants (CNVs).

m-HMM

• Description : m-HMM is a tool to detect copy number variation (CNV) in next-generation sequencing (NGS). The m-HMM algorithm uses a hidden Markov model (HMM) together with emission probabilities that are directed by mixture distributions, and it estimates the parameter values applying the Expectation-Maximization (EM) algorithm.

Magnolya

• Description : Magnolya is a tool to detect copy number variation (CNV) within two individual genome sequences. The Magnolya algorithm uses a Poisson mixture model to identify CNV between two genomes by joining the strings into a single assembly, creates a graph, and traverses the edges and nodes to infer the CNV probabilities. This approach eliminates the need for segmentation of the genomic regions and mapping to a reference genome.

MATCHCLIP

• Description : A legacy tool for detecting copy number variation (CNV) breakpoints. The algorithm identified the breakpoint CIGAR strings of reads and their positions. See links for the updated version.

matchclips2

• Description : An updated version of matchclips for detecting copy number variation (CNV) breakpoints. The algorithm identified the breakpoint CIGAR strings of reads and their positions. The updated algorithm runs much faster than the original one.

mBPCR

• Description : mBPCR is an R tool for estimating copy number variation (CNV) using Bayesian Piecewise Constant Regression.

Mercury-NHGRI

• Description : Mercury is a pipeline for detection of homozygous/hemizygous copy number variation (CNV) in data from Mendelian disease cohorts. Mercury uses the algorithm implemented in HMZDelFinder (see links).

MGP-HMM

• Description : MGP-HMM is a tool for detecting copy number variation (CNV). The MGP-HMM algorithm uses a hidden Markov Model (HMM) to discriminate copies from duplicated in tandem from other repeats and, also, a Poisson distribution to model the read depth and to estimate CNV lengths.

MixClone

• Description : MixClone is a tool to infer and study subclonal structures of tumor genomes structural variation, such as subclonal cellular prevalences, allelic configuration, copy number estimation. The MixClone package also includes visualization tools. The MixClone algorithm uses a unique probabilistic mixture model to infer predominances of subclonal cell populations from whole-genome sequencing (WGS) data.

MixHMM

• Description : MixHMM is a tool for inferring copy number variation (CNV) and allelic imbalance from single nucleotide polymorphism (SNP) array data. The MixHMM algorithm uses a unique hidden Markov model (HMM) for chromosomal structural aberrations as hidden states and an innovative sample mixing design to detect tumor CNV in heterogeneous samples.

MLPAstats

• Description : MLPAstats is an R package to analyse and visualize copy number variation (CNV) in Multiplex-Dependent Probe Amplification (MLPA) data.

modSaRa

• Description : modSaRa is an R package to identify copy number variable (CNV) segments in genomic data. modSaRa is a modified version of SaRa. See 'links'.

modSaRa2

• Description : modSaRa2 is an R package to identify copy number variable (CNV) segments in genomic data. modSaRa2 is an improved version of modSaRa by the integration of relative allelic intensity data to reduce noise.

MSeq-CNV

• Description : MSeq-CNV is an R program to detect copy number variation (CNV) from Sequencing based on Multiple samples. The algorithm uses a mixture density and models the number of mate-pairs using binomial distribution accounting for the insertion size and a Poisson distribution in each genomic position for computing the read counts. MSeq-CNV is well suited for diploid NGS data.

multiSaRa

• Description : modSaRa2 is an R package to identify copy number variable (CNV) segments in multiple sequences.

Nano-GLADIATOR

• Description : Nano-GLADIATOR (Nanopore Genomic aLterations AnD allelIc frAcTiOn pRedictor) is a tool for detecting copy number variation (CNV) in nanopore sequencing data (MinION/GridION).

NanoStringNormCNV

• Description : NanoStringNormCNV is a tool for pre-processing and copy number variation (CNV) calling from NanoString data. The algorithm obtains a cohort mean by computing sample averages and normalized to obtain sample-specific data. It detects CNVs from count ratios of probes or genes and uses kernel density to compute thresholds, that are either set or dynamically computed range for pooled reference.

ONCOCNV

• Description : ONCOCNV is a tool to detect copy number variation (CNV) in ultra-deep targeted sequencing. The algorithm uses multifactor normalization and annotation techniques to detect large copy number variation in amplicon sequencing data. The Authors claim their method to have comparable precision to CGH techniques.

panelcn.MOPS

• Description : A tool for the detection of copy number variation (CNV) in Next Generation Sequencing (NGS) data panels. This tool includes QC criteria for samples and for a region of interest. Implemented as a standalone tool with a graphical user interface for clinical diagnostics usage and as an R package.

ParseCNV

• Description : ParseCNV is a tool to associate copy number variation (CNV) in case-control design and family-based studies. The ParseCNV algorithm also implements quality control.

Patchwork

• Description : A tool for analysis and visualization of allele-specific copy number variation (CNV) and loss-of-heterozygosity (LOH) in cancer genomes. The Patchwork tool comes in two variants, Patchwork which takes BAM files as input and PatchworkCG takes CompleteGenomics files as input.
  Alternative name: patchworkCG.

PennCNV2

• Description : PennCNV2 is a tool for detecting copy number variation (CNV) from single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. The tool used the maximum likelihood method and the Hidden Markov Model (HMM) to include and integrate allele-specific SPN intensity and physical maps for posterior inference of copy number alterations.
  Alternate names: PennCNV-tumor, PennCNV

PICNIC

• Description : PICNIC is a software tool to predict copy number variation (CNV) in microarray cancer data. The PICNIC algorithm uses a unique preprocessing transformation and a hidden Markov Model (HMM) which is specific to cancer data. It classifies genotypes, specifies regions of loss of heterozygosity (LOH), and produces allelic copy number segmentation.

PlatinumCNV

• Description : PlatinumCNV is a tool for detecting allele-specific copy number variation (CNV) from single nucleotide (SNP) array data. The algorithm uses a Bayesian Gaussian mixture model.

PSE-HMM

• Description : PSE-HMM is a tool to detect copy number variation (CNV) in next-generation sequencing (NGS) data with mate-pairs. The PSE-HMM algorithm uses position-specific, a Gaussian mixture distribution, to model CNVs.

PureCN

• Description : PureCN package is for detection of copy number variation (CNV) and single nucleotide variation classification in targeted sequencing data. The PureCN algorithm estimates tumor purity, CNV, loss of heterozygosity (LOH), contamination, and classifies single nucleotide variants (SNVs) by somatic status and clonality. The algorithm integrates well with various somatic variant detection pipelines.

PyLOH

• Description : PyLOH is a tool for detecting copy number variation (CNV) and loss of heterozygosity in cancer genomes. The algorithm uses a unified probabilistic framework.

QDNAseq and HiC

• Description : QDNAseq and HiC are R scripts to detect, characterize copy number variation (CNV) and chromosomal rearrangements in human tumor samples. These scripts use Hi-C data.

QuantiSNP

• Description : QuantiSNP is a tool to identify copy number variation (CNV) in Illumina Infinium I/II SNP, Affymetrix 500K and SNP 6.0 genotyping data. The tool is available, but no longer maintained, since May 31st, 2011..

ReadDepth

• Description : ReadDepth is an R package to detect copy number variation (CNV) in short-read sequencing data. The ReadDepth algorithm uses a statistical model to account for overdispersed data and does not need reference sample data.

RefCNV

• Description : A tool to copy number variation (CNV). The algorithm uses a reference set to estimate the sequence coverage of each exon.

rSW-seq

• Description : rSW-seq is a tool to detect copy number variation (CNV). The rSW-seq method uses the Smith-Waterman local alignment algorithm with single-end sequencing data as the basis. The tool is available from the Authors upon request.

RUbioSeq

• Description : RUbioSeq is an integrated software suite for primary and secondary analysis of single nucleotide (SNP), copy number variants (CNV), and bisulfite-seq analyses.

RUbioSeq+

• Description : RUbioSeq+ is an updated and extended version of RUbioSeq. It is an integrated software suite for primary and secondary analysis of single nucleotide (SNP), copy number variants (CNVs), and bisulfite-seq analyses. The extended version includes a pipeline for ChIP-seq experiments, DNA-seq experiments, improvements in the parallelization, and multithreading.

SAAS-CNV

• Description : SAAS-CNV is a tool to identify somatic copy number variation (CNV) in next-generation sequencing (NGS) data. The SAAS-CNV algorithm consists of four main steps: (1) reading a reference and alleles at each locus for comparison of the read depth and alleles with tumor and healthy samples, (2) joint segmentation on the two signals, (3) correction of the CNV baseline, (4) calling of somatic CNVs for all detected signals.

SAD

• Description : SAD (Segmentation Analysis of DNA) is a tool for analysis of copy number variation (CNV). The SAD algorithm applies measurement theory, clustering algorithms, and uncomplicated, robust statistics in the interpretation of the analytical relations. The tool may be available by request (see contact).

SaRa

• Description : A tool to detect and rank copy number variation (CNV). A modified version, modSaRa and modSaRa2 are also available.

sCNAphase

• Description : sCNAphase is a tool for genotyping copy number variation (CNV) in haplotype resolved whole-genome sequencing data. The sCNAphase algorithm designed is for the analysis of low cellularity aneuploid tumors.

SCNVSim

• Description : SCNVSim is a software tool for simulation of somatic copy number variation (CNV) and structural sequence variations, such as aneuploidy, heterogeneity, and purity.

SEG

• Description : SEG is a tool to detect copy number variation (CNV) in whole-genome cancer sequencing data. The SEG algorithm normalizes the data by computing the log-ratio of normal and tumor density and finds points of difference by a Dynamic Programming method.

SegCNV

• Description : A tool for the detection of copy number variation (CNV) in single nucleotide polymorphism (SNP) arrays, particularly designed for germline data. SegCNV supports Illumina 550K and 610K genotyping platforms. The algorithm uses log R ratios (LRR) and B allele frequencies (BAF) for the detection.

SelEstim

• Description : Software to detect signatures of selection from gene frequency data and measure the selection intensity.

seqCNA

• Description : Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization.

SeqSeg

• Description : A Matlab tool for detection and localization of copy number variation (CNV).

Sequenza

• Description : Sequenza package provides tools to genotyping cancer samples, cancer cellularity, ploidy, copy number variation (CNV), and infer alleles that are mutated.

ShinyCNV

• Description : ShinyCNV is a tool for visualization of copy number variation (CNV) and single nucleotide polymorphism (SNP) data from Illumina and Affymetrix platforms. Users can both automatically and semi-manually edit the data.

SMURF-seq

• Description : SMURF-seq is a collection of R and Python scripts for sequencing short reads for copy number variation (CNV) profiling.

STAC

• Description : STAC is a tool for testing the significance of DNA copy number variation (CNV). The STAC method uses two separate statistics, and it computes the final P-values by multiple testing corrected permutations.

SubPatCNV

• Description : SubPatCNV is a tool for discovery/identification of copy number variable (CNV) regions larger than a set threshold. The algorithm uses approximate pattern matching for the identification of CNVs.

SWITCHdna

• Description : SWITCHdna is an R library for detection of copy number variation (CNV). The algorithm is based on intensity data from copy number platforms, identifies transition points, and tests the significance using Fisher's exact test, Chi-square approximations, and Wilcoxon rank-sum tests. The library includes a function for visualization of data.

SynthEx

• Description : SynthEx is a tool to detect copy number alteration (CNA) and to profile tumor heterogeneity in a variety of high-throughput sequencing data. The SynthEx algorithm uses "synthetic normal" to represent the target; Thus, it does not need a matched pair of samples as normals.

TAGCNA

• Description : TAGCNA is a tool written in R for identification of significant consensus events in cancer genomes using copy number variation (CNV). The algorithm uses 'a peel-off' permutation scheme for modeling a null distribution.

TITAN

• Description : TITAN is a tool for estimation of copy number variation (CNV) and loss of heterozygosity (LOH) in whole-genome sequencing data consisting of clonal cell populations. The TITAN algorithm uses hidden Marlov model (HMM).
  Alternative name: TitanCNA

TrioCNV

• Description : TrioCNV is a tool designed for the detection of copy number variation (CNV), jointly occurring in parents and offsprings. The algorithm uses negative binomials regression, evaluates GC content and mappability biases, constrained by Mendelian inheritance, and combines these models using Hidden Markov Model (HMM).

VCF2CNA

• Description : VCF2CNA is a tool to detect copy number variation (CNV) in Tumor/Germline Variant Call Format (VCF) files. The VCF2CNA algorithm also computes tumor purity estimates for samples.

VCS

• Description : A tool for visualizing copy number variation (CNV) and single nucleotide polymorphism (SNP) data. VCS can visualize the enrichment of genome contents in CNV, CNV and/or SNP physical distribution, the log 2 CNV distribution ratio, the number of CNVs and SNPs per binning, homozygosity distribution of genotypes, and a cytomap of genes.

WaveCNV

• Description : WaveCNV is a software tool package to detect copy number variation (CNV). The WaveCNV algorithm uses translation-invariant discrete wavelet transforms to detect CNV breakpoints in next-generation sequencing (NGS) data. It also assigns alleles and determines the chromosomal ratio following duplication or loss.
  Alternative names: WaveCNV-caller, WaveCNV-segmenter.

waviCGH

• Description : waviCGH is a web-based tool for the analysis and comparison of genomic copy number variation (CNV) in varied species.

WISARD

• Description : WISARD, a Workbench for Integrated Superfast Association study with Related Data is a statistical analysis toolkit for the analysis of large-scale single nucleotide polymorphism (SNP), copy number variation (CNV), and next-generation sequencing (NGS) data. With WISARD you can analyze related and unrelated samples. The code is optimized for running in multi-core CPUs.

WISECONDOR

• Description : Wisecondor (WIthin-SamplE COpy Number aberration DetectOR) is a tool for detecting copy number variation (CNV) in low coverage whole-genome sequencing data. Wisecondor is designed and limited for use in prenatal diagnosis. The algorithm uses a normalization technique within samples.

WisecondorX

• Description : WisecondorX is a tool for detecting copy number variation (CNV) in low coverage whole-genome sequencing data. It is an improved version of Wisecondor. The algorithm uses a normalization technique within samples.

wuHMM

• Description : wuHMM (Washington University Hidden Markov Model) is a tool for copy number variation (CNV) detection. It uses data from comparative genomic hybridization (aCGH). Also, the wuHMM algorithm can assign CNV regions into discrete genotypes.

XCAVATOR

• Description : XCAVATOR is a tool for detection of copy number variation (CNV) in whole-genome sequencing data. The XCAVATOR algorithm uses Poisson distribution to model the sequencing depth.

YMAP

• Description : YMAP is a pipeline for detection and analysis of custom copy number variation (CNV), single nucleotide polymorphism (SNP) and loss of heterozygosity (LOH). YMAP makes figures, a summary of the analyses and displays them on a web page.

Zinfandel

• Description : Zinfandel is a tool designed for detection of copy number variation (CNV) in low coverage data. It uses Hidden Markov Model (HMM) to estimate the coverage from multiple mate-pairs without designating single mate-pairs as outliers.

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