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Somatic SNV detection software tools | High-throughput sequencing

High-throughput sequencing software tools > Whole-genome sequencing software tools

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 (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Source text: Roberts et al., 2013.

Bambino

OMIC_00876

Bambino

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

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 advantage of SAM-specific annotations, and produces…

Bassovac

OMIC_05102

Bassovac

Improved Bayesian inversion somatic caller.

Improved Bayesian inversion somatic caller.

Cake

OMIC_03613

Cake

A bioinformatics software pipeline that integrates four publicly available somatic…

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 algorithm alone.

CAN and LOH Assessment in Impure and Aneuploid…

OMIC_04173

CAN and LOH Assessment in Impure and Aneuploid Tumors
CLImAT

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

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

DeNovoGear

OMIC_00083

DeNovoGear

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

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 discovery in exome analysis and fragment information to…

Empirical Baysian mutation Calling

OMIC_00084

Empirical Baysian mutation Calling
EBCall

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

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

FaSD-somatic

OMIC_04051

FaSD-somatic

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

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

HapMuC

OMIC_05379

HapMuC

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

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

JointSNVMix

OMIC_00085

JointSNVMix

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

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

LocHap

OMIC_10162

LocHap

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

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 LH exhibits more than two genotypes, we call it a…

LoLoPicker

OMIC_11396

LoLoPicker

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

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 requires users to provide a control panel…

MSIsensor

OMIC_02192

MSIsensor

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

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

multiSNV

OMIC_07650

multiSNV

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

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 matched normal, multiSNV jointly considers all…

mutationSeq

OMIC_00086

mutationSeq

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

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

MuTect

OMIC_00087

MuTect

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

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.

Polymutt

OMIC_00088

Polymutt

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

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 detection and genotyping of SNPs, Polymutt can…

qSNP

OMIC_00089

qSNP

A single nucleotide variant caller optimised for identifying somatic variants in low…

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

QuadGT

OMIC_02108

QuadGT

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

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

RAre REference VAriant annotaTOR

OMIC_08308

RAre REference VAriant annotaTOR
RAREVATOR

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

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 UnifiedGenotyper module of GATK for genotyping all the…

RNA and DNA Integrated Analysis

OMIC_08675

RNA and DNA Integrated Analysis
RADIA

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

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, especially at low DNA allelic frequencies.

RVD2

OMIC_08321

RVD2

A variant calling algorithm that uses a hierarchical Bayesian model to estimate allele…

A variant calling algorithm that uses a hierarchical Bayesian model to estimate allele frequency and call variants in heterogeneous samples. RVD2 improves upon current classifiers and has higher sensitivity and specificity over a wide range of…

SAMtools

OMIC_00090

SAMtools

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

A suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format), BCFtools (Reading/writing BCF2/VCF/gVCF files and…

Shimmer

OMIC_03612

Shimmer

Detects somatic single-nucleotide variants using statistical hypothesis testing with…

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

SNV-PPILP

OMIC_06794

SNV-PPILP

A fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for…

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 lp_solve.

SNVMix

OMIC_00077

SNVMix

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

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

SOAPsnv

OMIC_04229

SOAPsnv

A software package for detecting somatic mutation of single nucleotide variant (SNV) by…

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

SomaticCall

OMIC_02155

SomaticCall

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

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 positive rate. SomaticCall takes as input a BAM file for…

SomaticSeq

OMIC_10002

SomaticSeq

An accurate somatic mutation detection pipeline implementing a stochastic boosting…

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 and deletions. The workflow currently…

SomaticSniper

OMIC_00092

SomaticSniper

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

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).

SomVarIUS

OMIC_10714

SomVarIUS

A computational method for detecting somatic variants using high throughput sequencing…

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 and real tumor samples. SomVarIUS identifies…

Strelka

OMIC_00093

Strelka

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

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

VariantMaster

OMIC_02261

VariantMaster

Extract causative variants for monogenic and sporadic genetic diseases.

Extract causative variants for monogenic and sporadic genetic diseases.

VarScan

OMIC_00094

VarScan

A platform-independent mutation caller for targeted, exome, and whole-genome resequencing…

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 2, is written in Java, so it runs on most…

Virmid

OMIC_00095

Virmid

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

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