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Somatic copy-number alteration detection software tools | Whole-genome 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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SegSeq
Desktop

SegSeq

A computational algorithm to detect and localize copy-number alterations from…

A computational algorithm to detect and localize copy-number alterations from massively parallel sequence data. SegSeq is a hybrid of local change-point analysis with a subsequent merging procedure…

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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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BIC-seq
Desktop

BIC-seq

Combines normalization of the data at the nucleotide level and Bayesian…

Combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline copy number variations (CNVs) accurately. Whereas…

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CONSERTING
Desktop
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Patchwork
Desktop

Patchwork

A bioinformatic tool for analyzing and visualizing allele-specific copy numbers…

A bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which…

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sCNAphase
Desktop

sCNAphase

An R package, designed for estimating tumor copy number profile, tumor…

An R package, designed for estimating tumor copy number profile, tumor cellularity, tumor ploidy, based on whole genome sequencing (WGS) or whole exome sequencing (WES) data. sCNAphase integrates…

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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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HMMcopy
Desktop

HMMcopy

A suite of tools to make copy number estimations for whole genome data with GC…

A suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed…

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iGC
Desktop

iGC

Identifies differentially expressed genes driven by Copy Number Alterations…

Identifies differentially expressed genes driven by Copy Number Alterations (CNA) from samples with both gene expression and CNA data. iGC supports multiple input formats and users can define their…

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HATS
Desktop

HATS Haplotype Amplification in Tumor Sequences

A tool that calls the amplified alleles, and thus amplified haplotype, in copy…

A tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next-generation sequencing tumor data. The amplified haplotype may reveal gene variants. We…

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FACETS
Desktop

FACETS Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing

An allele-specific copy number analysis (ASCN) tool and open-source software…

An allele-specific copy number analysis (ASCN) tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. FACETS provides a…

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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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CNAnorm
Desktop

CNAnorm

A normalization method for copy number aberration in cancer samples. CNAnorm…

A normalization method for copy number aberration in cancer samples. CNAnorm performs ratio, GC content correction and normalization of data obtained using very low coverage (one read every…

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CNAseg
Desktop

CNAseg

A framework for the identification of CNA events that uses flowcell-to-flowcell…

A framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses…

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SoloDel
Desktop

SoloDel Somatic Low-frequent Deletion call model

A Java based somatic deletion caller designed for whole-genome sequencing data…

A Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling…

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AbsCN-seq
Desktop

AbsCN-seq

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers…

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data. A simulation study shows that estimates have reasonable…

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WaveCNV
Desktop

WaveCNV

A software package to identify copy number alterations by detecting breakpoints…

A software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using…

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COPS
Desktop

COPS COpy number using Paired Samples

An accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs…

An accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from…

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OncoSNP-SEQ
Desktop

OncoSNP-SEQ

An analytical tool for characterizing copy number alterations and…

An analytical tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.

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SV-Bay
Desktop

SV-Bay

Detects structural variants in cancer using whole genome sequencing data with…

Detects structural variants in cancer using whole genome sequencing data with or without matched normal control sample. SV-Bay does not only use information about abnormal read mappings but also…

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Segmentum
Desktop

Segmentum

Segments the genome by analyzing the read-depth and B-allele fraction profiles…

Segments the genome by analyzing the read-depth and B-allele fraction profiles using a double sliding window method. Segmentum is a tool for the identification of copy number alterations (CNAs) and…

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seqCNA
Desktop

seqCNA

A parallelized R package for an integral copy number analysis of…

A parallelized R package for an integral copy number analysis of high-throughput sequencing cancer data. seqCNA includes novel methodology on (i) filtering, reducing false positives, and (ii) GC…

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rSW-seq
Desktop

rSW-seq

A method for identification of copy number alterations in a tumor genome…

A method for identification of copy number alterations in a tumor genome compared to its matched control, based on application of Smith-Waterman algorithm to single-end sequencing data. In a…

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VCF2CNA
Web

VCF2CNA

Detects copy number alteration (CNA). VCF2CNA is a web-based tool capable of…

Detects copy number alteration (CNA). VCF2CNA is a web-based tool capable of accurate and efficient detection of CNAs from variants called from high-coverage wide genome sequencing (WGS) data…

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SomatiCA
Desktop

SomatiCA

A package that is capable of identifying, characterizing and quantifying SCNAs…

A package that is capable of identifying, characterizing and quantifying SCNAs from cancer genome sequencing. By directly accounting for tumor purity and subclonality, SomatiCA was especially…

Copy Number…
Desktop
Web

Copy Number Explorer

An interactive tool for mining large copy number datasets. Copy Number Explorer…

An interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most…

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