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…
Desktop app
G T A T C G C T A SAMtools SAMtools

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…

Desktop app
G T A T C G C T A MuTect MuTect

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.

Desktop app
G T A T C G C T A VarScan VarScan

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…

Desktop app
G T A T C G C T A DeNovoGear DeNovoGear

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…

Desktop app
G T A T C G C T A SomaticSniper SomaticSniper

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).

Desktop app
G T A T C G C T A SNVMix SNVMix

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.

Desktop app
G T A T C G C T A JointSNVMix JointSNVMix

JointSNVMix

Implements a probabilistic graphical model to analyse sequence data from…

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

Desktop app
G T A T C G C T A Empirical Baysian… Empirical Baysian mutation Calling

EBCall Empirical Baysian mutation Calling

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

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

Desktop app
G T A T C G C T A Virmid Virmid

Virmid

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

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

Desktop app
G T A T C G C T A Polymutt Polymutt

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…

Desktop app
G T A T C G C T A mutationSeq mutationSeq

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.

Desktop app
G T A T C G C T A Bambino Bambino

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…

Desktop app
SNooPer SNooPer

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…

Desktop app
G T A T C G C T A RNA2DNAlign RNA2DNAlign

RNA2DNAlign

A computational framework that can evaluate evidence of allelic imbalance and…

A computational framework that can evaluate evidence of allelic imbalance and asymmetry of DNA and RNA sequencing datasets. RNA2DNAlign identifies allelic distributions corresponding to the following…

Desktop app
G T A T C G C T A SiNVICT SiNVICT

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…

Desktop app
G T A T C G C T A VarDict VarDict

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…

Desktop app
G T A T C G C T A MuSE MuSE

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 data. MuSE models the evolution of the reference allele to the allelic composition of the matched tumor…

Desktop app
G T A T C G C T A LoLoPicker LoLoPicker

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…

Desktop app
G T A T C G C T A SomVarIUS SomVarIUS

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…

Desktop app
G T A T C G C T A LocHap LocHap

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…

Desktop app
G T A T C G C T A SomaticSeq SomaticSeq

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…

Desktop app
G T A T C G C T A RNA and DNA… RNA and DNA Integrated Analysis

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,…

Desktop app
G T A T C G C T A RVD2 RVD2

RVD2

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

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…

Desktop app
G T A T C G C T A RAre REference… RAre REference VAriant annotaTOR

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…

Desktop app
G T A T C G C T A multiSNV multiSNV

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…

Desktop app
G T A T C G C T A SNV-PPILP SNV-PPILP

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…

Desktop app
G T A T C G C T A HapMuC HapMuC

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.

Desktop app
G T A T C G C T A Bassovac Bassovac

Bassovac

Improved Bayesian inversion somatic caller.

Improved Bayesian inversion somatic caller.

Desktop app
G T A T C G C T A SOAPsnv SOAPsnv

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.

Desktop app
G T A T C G C T A CAN and LOH… CAN and LOH Assessment in Impure and Aneuploid…

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.

Desktop app
G T A T C G C T A FaSD-somatic FaSD-somatic

FaSD-somatic

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

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

Desktop app
G T A T C G C T A Cake Cake

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…

Desktop app
G T A T C G C T A Shimmer Shimmer

Shimmer

Detects somatic single-nucleotide variants using statistical hypothesis testing…

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

Desktop app
G T A T C G C T A VariantMaster VariantMaster

VariantMaster

Extract causative variants for monogenic and sporadic genetic diseases.

Extract causative variants for monogenic and sporadic genetic diseases.

Desktop app
G T A T C G C T A MSIsensor MSIsensor

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.

Desktop app
G T A T C G C T A QuadGT QuadGT

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.

Desktop app
G T A T C G C T A Strelka Strelka

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.

Desktop app
G T A T C G C T A qSNP qSNP

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.

Desktop app
G T A T C G C T A SomaticCall Deprecated SomaticCall

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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