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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.

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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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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed…

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles…

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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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Strelka
Desktop

Strelka

Provides analysis of germline variation in small cohorts and somatic variation…

Provides analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Strelka is a variant calling method building upon the innovative Strelka somatic variant…

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Virmid
Desktop

Virmid

Estimate sample composition accurately or the level of contamination of a…

Estimate sample composition accurately or the level of contamination of a disease sample without genotyping. Virmid is a probabilistic method for Single Nucleotide Variation (SNV) calling. This…

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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

Extracts causative variants in familial and sporadic genetic diseases.…

Extracts causative variants in familial and sporadic genetic diseases. VariantMaster implements a methodology to evaluate the status (presence or absence) of a variant in familial or case-control…

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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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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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ISOWN
Desktop

ISOWN Identification of SOmatic mutations Without matching Normal tissues

Predicts somatic mutations from tumor only samples. ISOWN is an algorithm that…

Predicts somatic mutations from tumor only samples. ISOWN is an algorithm that uses supervised machine learning to distinguish simple substitution somatic mutations in coding regions from germline…

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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

Detects somatic mutations. EBCall is a statistical framework using a massively…

Detects somatic mutations. EBCall is a statistical framework using a massively parallel sequencing of the cancer genome and explicitly taking into account prior information of sequencing errors. The…

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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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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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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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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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pyAmpli
Desktop

pyAmpli

Corrects moderate true positive rates and allows reduction of high false…

Corrects moderate true positive rates and allows reduction of high false positive rates observed in polymerase chain reaction (PCR)-based targeted enrichment strategies. pyAmpli exploits amplicon…

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Lancet
Desktop

Lancet

Assembles jointly reads from a tumor and a matched normal sample into graphs.…

Assembles jointly reads from a tumor and a matched normal sample into graphs. Lancet is a somatic single nucleotide variant (SNV) and indel caller which uses localized colored DeBruijn graphs to…

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GVC
Desktop

GVC Genomic Variant Caller

Detects various genomic variants including single nucleotide variant (SNV),…

Detects various genomic variants including single nucleotide variant (SNV), single insertion/deletion (sINDEL) and structural variation (SV) from personal and normal-cancer paired whole-genome/exome…

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TSNAD
Desktop

TSNAD

Identifies cancer somatic mutations following the best practices of the genome…

Identifies cancer somatic mutations following the best practices of the genome analysis toolkit (GATK) from the genome/exome sequencing data of tumor-normal pairs. TSNAD is an integrated software…

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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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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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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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PDAC Disease Models
Desktop

PDAC Disease Models Pancreatic Ductal AdenoCarcinoma Disease Models

Provides a pipeline for analyzing whole-genome sequencing (WGS) data for simple…

Provides a pipeline for analyzing whole-genome sequencing (WGS) data for simple somatic mutation (SSM), structural variation (SV) and copy number variation (CNV). PDAC Disease Models is a R package…

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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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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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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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ExScalibur-SMD
Desktop

ExScalibur-SMD

Allows users to analyze exome data. ExScalibur-SMD provides a method that uses…

Allows users to analyze exome data. ExScalibur-SMD provides a method that uses multiple alignment and variant detection algorithms to perform complex and computationally-demanding data analysis. It…

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ExScalibur
Desktop

ExScalibur

Discovers germline and somatic mutations in the human genome. ExScalibur…

Discovers germline and somatic mutations in the human genome. ExScalibur consists in a set of scalable whole exome sequencing (WES) analysis program highly configurable. It aims to assist researchers…

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V-pipe
Desktop

V-pipe

Allows users to study clinical applications of next generation sequencing (NGS)…

Allows users to study clinical applications of next generation sequencing (NGS) data.

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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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