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75 Free Copy Number Variation (CNV) Analysis Tools - Software and Resources

75 Free Copy Number Variation (CNV) Analysis Tools - Software and Resources

Graph: The word 'CNV' occurences in scientific articles stored in PubMed from 1990 to June 2019.
The word "CNV" occurences in scientific articles stored in PubMed from 1990 to December 2018.

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  1. 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.
  2. 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
  3. 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.
  4. Ensembl 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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'.
  10. 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.
  11. 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.
  12. CNVcaller
    • Description : Program for detecting the integrated copy number veriation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria. The result is a VCF format genotype file which can be used in GWAS/QLT research.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. ADTEx
    • Description : A tool for detection of copy number variation (CNV) in whole-genome exome data from paired or normal tumor samples. The tool implements Hidden Markov Models (HMM) in the prediction of CNV number, genotypes, polyploid, aneuploidy, cell contamination, and baseline shifts.
  26. 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.
  27. AneuFinder
    • Description : AneuFinder is an R package for copy number variation (CNV) detection, breakpoint detection, karyotype, and heterogeneity analysis between single cells.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. SeqSeg
    • Description : A Matlab tool for detection and localization of copy number variation (CNV).
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. CNVtools
    • Description : CNVtools is an R package designed for testing of copy number variation (CNV) data to facilitate association studies.
  42. 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.
  43. 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).
  44. SaRa
    • Description : A tool to detect and rank copy number variation (CNV). A modified version, modSaRa and modSaRa2 are also available.
  45. 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.
  46. 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).
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. multiSaRa
    • Description : modSaRa2 is an R package to identify copy number variable (CNV) segments in multiple sequences.
  54. ClinTAD
    • Description : A tool for interpretation of copy number variation (CNV) in the context of topologically associated domains (TADs).
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. CCRET
    • Description : A tool to detect copy number variation (CNV). The algorithm models the effects of CNV features in multiple categories..
  66. RefCNV
    • Description : A tool to copy number variation (CNV). The algorithm uses a reference set to estimate the sequence coverage of each exon.
  67. 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.
  68. 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.
  69. CNVtest
    • Description : An R tool for testing copy number variation (CNV) association based on log-ratio data of SNP arrays.
  70. LRS
    • Description : A tool for selecting a likelihood ratio based on SNP Chip LogR data for copy number variants (CNVs).
  71. 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.
  72. 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.
  73. 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.
  74. 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.
  75. 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.

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