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
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
Bassovac
Improved Bayesian inversion somatic caller.
Improved Bayesian inversion somatic caller.
Cake
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…
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
VariantMaster
Extract causative variants for monogenic and sporadic genetic diseases.
Extract causative variants for monogenic and sporadic genetic diseases.
VarScan
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
Virmid
A Java based variant caller designed for disease-control matched samples.
A Java based variant caller designed for disease-control matched samples.