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Somatic single nucleotide variant detection software tools | Whole-genome sequencing data analysis

With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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MuTect
Desktop

MuTect

A method developed at the Broad Institute for the reliable and accurate…

A method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

SNooPer
Desktop

SNooPer

A versatile machine learning approach that uses Random Forest classification…

A versatile machine learning approach that uses Random Forest classification models to accurately call somatic variants in low-depth sequencing data. SNooPer uses a subset of variant positions from…

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GATK…
Desktop

GATK UnifiedGenotyper

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian…

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype likelihood model to estimate simultaneously the most likely genotypes and allele frequency in a population of N…

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DeNovoGear
Desktop

DeNovoGear

A software tool for analyzing de novo mutations from familial and somatic…

A software tool for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation…

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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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Nanopolish
Desktop

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov…

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format…

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marginAlign
Desktop

marginAlign

The package can be used to align reads to a reference genome and call single…

The package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads. The package comes with two programs:…

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Virmid
Desktop

Virmid

A Java based variant caller designed for disease-control matched samples.

A Java based variant caller designed for disease-control matched samples.

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RNA2DNAlign
Desktop

RNA2DNAlign

Evaluates evidence of allelic imbalance and asymmetry of DNA and RNA sequencing…

Evaluates evidence of allelic imbalance and asymmetry of DNA and RNA sequencing datasets. RNA2DNAlign identifies allelic distributions corresponding to the following events: RNA editing (RNAed),…

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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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VariantMaster
Desktop

VariantMaster

Extract causative variants for monogenic and sporadic genetic diseases.

Extract causative variants for monogenic and sporadic genetic diseases.

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Bambino
Desktop

Bambino

A variant detector and graphical alignment viewer for next-generation…

A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes…

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Strelka
Desktop

Strelka

A method for somatic SNV and small indel detection from sequencing data of…

A method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples.

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SomaticSniper
Desktop

SomaticSniper

The purpose of this program is to identify single nucleotide positions that are…

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files).

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multiSNV
Desktop

multiSNV

A software package for calling single nucleotide variants (SNVs) using NGS data…

A software package for calling single nucleotide variants (SNVs) using NGS data from multiple same-patient samples. Instead of performing multiple pairwise analyses of a single tumour sample and a…

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SiNVICT
Desktop

SiNVICT

A computational method that detects single nucleotide variants (SNVs) and short…

A computational method that detects single nucleotide variants (SNVs) and short indels from circulating cell-free DNA (cfDNA) sequencing data. SiNVICT increases the sensitivity and specificity of SNV…

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SNVMix
Desktop

SNVMix

It is designed to detect single nucleotide variants from next generation…

It is designed to detect single nucleotide variants from next generation sequencing data.

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MuSE
Desktop

MuSE

A somatic point mutation caller for tumor-normal paired samples in…

A somatic point mutation caller for tumor-normal paired samples in next-generation sequencing (NGS) data. MuSE models the evolution of the reference allele to the allelic composition of the matched…

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Mutascope
Desktop

Mutascope

A sequencing analysis pipeline specifically developed for the identification of…

A sequencing analysis pipeline specifically developed for the identification of somatic variants present at low-allelic fraction from high-throughput sequencing of amplicons from matched tumor-normal…

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JointSNVMix
Desktop

JointSNVMix

Implements a probabilistic graphical model to analyse sequence data from…

Implements a probabilistic graphical model to analyse sequence data from tumour/normal pairs.

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EBCall
Desktop

EBCall Empirical Baysian mutation Calling

A software package for somatic mutation detection (including InDels).

A software package for somatic mutation detection (including InDels).

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Polymutt
Desktop

Polymutt

Implement a likelihood-based framework for calling single nucleotide variants…

Implement a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. In addition to facilitating…

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LocHap
Desktop

LocHap

An ultra-fast computational pipeline that searches for multiple single…

An ultra-fast computational pipeline that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an…

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MosaicHunter
Desktop

MosaicHunter

Detects postzygotic single-nucleotide mosaicism (SNMs) through next-generation…

Detects postzygotic single-nucleotide mosaicism (SNMs) through next-generation sequencing (NGS) of unpaired, trio, and paired samples. MosaicHunter is a software which integrates a Bayesian genotyper…

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MSIsensor
Desktop

MSIsensor

A C++ program for automatically detecting somatic and germline variants at…

A C++ program for automatically detecting somatic and germline variants at microsatellite regions.

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mutationSeq
Desktop

mutationSeq

A software suite using feature-based classifiers for somatic mutation…

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data.

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SomaticSeq
Desktop

SomaticSeq

An accurate somatic mutation detection pipeline implementing a stochastic…

An accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions…

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PopSV
Desktop

PopSV

Enables the systematic detection of Copy-Number Variations (CNVs) across the…

Enables the systematic detection of Copy-Number Variations (CNVs) across the genome. PopSV is an analytical method which detects abnormal read coverage using a set of samples as references. The…

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Shimmer
Desktop

Shimmer

Detects somatic single-nucleotide variants using statistical hypothesis testing…

Detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction.

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SomVarIUS
Desktop

SomVarIUS

A computational method for detecting somatic variants using high throughput…

A computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples. We evaluate the performance of the method using genomic data from synthetic…

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HapMuC
Desktop

HapMuC

A somatic mutation caller, which can utilize the information of heterozygous…

A somatic mutation caller, which can utilize the information of heterozygous germline variants near candidate mutations.

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Cake
Desktop

Cake

A bioinformatics software pipeline that integrates four publicly available…

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one…

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Cycledash
Web

Cycledash

Allows users to quickly filter, order, and examine variants. Cycledash is a web…

Allows users to quickly filter, order, and examine variants. Cycledash is a web application which facilitates the validation and analysis of somatic variants, bringing together and streamlining…

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SNV-PPILP
Desktop

SNV-PPILP

A fast and easy to use tool for refining GATK's Unified Genotyper SNV…

A fast and easy to use tool for refining GATK's Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny. SNV-PPILP is written in Python and requires the free ILP solver…

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RAREVATOR
Desktop

RAREVATOR RAre REference VAriant annotaTOR

A tool for the identification and annotation of germline and somatic variants…

A tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data. RAREVATOR is a Perl script that executes the…

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LoLoPicker
Desktop

LoLoPicker

An efficient tool dedicated to call somatic variants from whole-exome…

An efficient tool dedicated to call somatic variants from whole-exome sequencing data using tumor and its matched normal tissue, plus a user-defined control panel of non-cancer samples. The program…

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CLImAT
Desktop

CLImAT CAN and LOH Assessment in Impure and Aneuploid Tumors

A bioinformatic tool for identification of genome-wide aberrations from tumor…

A bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

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FaSD-somatic
Desktop

FaSD-somatic

A fast and accurate somatic single-nucleotide variations (SNVs) detection…

A fast and accurate somatic single-nucleotide variations (SNVs) detection program.

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RADIA
Desktop

RADIA RNA and DNA Integrated Analysis

A computational method combining the patient-matched normal and tumor DNA with…

A computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations,…

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SCoNEs
Desktop

SCoNEs Somatic Copy Number Estimator

Estimates the Copy Number Variation (CNV) in whole genome sequencing (WGS)…

Estimates the Copy Number Variation (CNV) in whole genome sequencing (WGS) paired cancer data. SCoNEs uses a read depth approach. The software aims to decipher the general LRR signal in set of…

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Bassovac
Desktop

Bassovac

Improved Bayesian inversion somatic caller.

Improved Bayesian inversion somatic caller.

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SOAPsnv
Desktop

SOAPsnv

A software package for detecting somatic mutation of single nucleotide variant…

A software package for detecting somatic mutation of single nucleotide variant (SNV) by re-sequencing.

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QuadGT
Desktop

QuadGT

A software package for calling single-nucleotide variants in four sequenced…

A software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents.

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LifeScope
Desktop

LifeScope

Leverages years of customer feedback and development for analysis tools for…

Leverages years of customer feedback and development for analysis tools for SOLiD system data, to enable faster translation of next-generation data to biologically meaningful results. Designed to…

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Sentieon TNseq
Desktop

Sentieon TNseq

Provides the same advantages over MuTect/MuTect2 as Sentieon DNAseq provides…

Provides the same advantages over MuTect/MuTect2 as Sentieon DNAseq provides over BWA-GATK: it is over 10X faster in core-hours, has no run-to-run difference, does no down-sampling in high coverage…

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qSNP
Desktop

qSNP

A single nucleotide variant caller optimised for identifying somatic variants…

A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples.

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SomaticCall
Desktop

SomaticCall

A program that finds single‐base differences (substitutions) between sequence…

A program that finds single‐base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false…

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