Insertion and deletion (indel) mutations, the most common type of structural variance in the human genome, affect a multitude of human traits and diseases. New sequencing technologies, such as deep sequencing, allow massive throughput of sequence data and greatly contribute to the field of disease causing mutation detection, in general, and indel detection, specifically. Source text: Neuman et al., 2013.
Assembly Based ReAligner
Assembly Based ReAligner
ABRA
It uses localized assembly and global realignment to align reads more accurately, thus…
It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
BreakDancer
BreakDancer
A Perl/C++ package that provides genome-wide detection of structural variants from next…
A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult…
BreakSeek
BreakSeek
A breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous…
A breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous and heterozygous INDELs, ranging from several base pairs to over thousands of base pairs, with accurate breakpoint and heterozygosity rate estimations.…
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…
Dindel
Dindel
A Bayesian method to call indels from short-read sequence data in individuals and…
A Bayesian method to call indels from short-read sequence data in individuals and populations by realigning reads to candidate haplotypes that represent alternative sequence to the reference. The candidate haplotypes are formed by combining…
Discovering Single Nucleotide Polymorphism
Discovering Single Nucleotide Polymorphism
discoSnp++
Detects both heterozygous and homozygous isolated SNPs from any number of read datasets,…
Detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate…
FermiKit
FermiKit
A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles…
A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions (INDELs) and structural variations (SVs). FermiKit…
FreeBayes
FreeBayes
A Bayesian genetic variant detector designed to find small polymorphisms, specifically…
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
GATK UnifiedGenotyper
GATK UnifiedGenotyper
A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype…
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 samples, emitting an accurate posterior probability…
HeurAA
HeurAA
Accurate and fast detection of genetic variations with a novel heuristic amplicon aligner…
Accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Illuminator
Illuminator
A sequence alignment program for the output from Illumina GA-II clonal sequencers.
A sequence alignment program for the output from Illumina GA-II clonal sequencers.
indelMINER
indelMINER
A set of algorithms and heuristics to identify indels from whole genome resequencing…
A set of algorithms and heuristics to identify indels from whole genome resequencing datasets using paired-end reads. indelMINER uses a split-read approach to identify the precise breakpoints for indels of size less than a user specified threshold,…
Indelocator
Indelocator
A software tool for calling short indels in next generation sequencing data.
A software tool for calling short indels in next generation sequencing data.
Manta
Manta
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta…
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and large insertions within a single workflow. The…
Mendelian-inheritance-AtTEntive…
Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder
MATE-CLEVER
An approach that accurately discovers and genotypes indels longer than 30 bp from…
An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or quartets, MATE-CLEVER integrates statistics that…
MoDIL
MoDIL
A novel method for finding medium sized indels from high throughput sequencing datasets.
A novel method for finding medium sized indels from high throughput sequencing datasets.
Pair Read Informed Split Mapper
Pair Read Informed Split Mapper
PRISM
A method that identifies SVs and their precise breakpoints from whole-genome resequencing…
A method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types,…
piCALL
piCALL
Identifies short indel polymorphisms in population sequencing data.
Identifies short indel polymorphisms in population sequencing data.
Pindel
Pindel
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem…
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequence data. Pindel uses a pattern growth approach to identify the…
PyroHMMvar
PyroHMMvar
A program to call short indels and SNPs for Ion Torrent and 454 data.
A program to call short indels and SNPs for Ion Torrent and 454 data.
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…
Scalpel
Scalpel
A software package for detecting INDELs (INsertions and DELetions) mutations in a…
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). Scalpel is designed to perform localized micro-assembly of…
Snippy
Snippy
Find SNPs/indels in a bacterial genome from NGS reads.
Find SNPs/indels in a bacterial genome from NGS reads.
SOAPindel
SOAPindel
Focusing on calling indels from the next-generation paired-end sequencing data.
Focusing on calling indels from the next-generation paired-end sequencing data.
SomaticIndelDetector
SomaticIndelDetector
The Somatic Indel Detector can be run in two modes: single sample and paired sample. In…
The Somatic Indel Detector can be run in two modes: single sample and paired sample. In the former mode, exactly one input bam file should be given, and indels in that sample are called. In the paired mode, the calls are made in the tumor sample,…
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…
SPLITREAD
SPLITREAD
A method for detecting INDELs (small insertions and deletion with size less than 50bp) as…
A method for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions deletions that are within the coding regions from the exome sequencing data.
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.
Structural Variant Machine
Structural Variant Machine
SV-M
Accurate indel prediction using paired-end short reads.
Accurate indel prediction using paired-end short reads.
Syzygy
Syzygy
SNP and indel calling for pooled and individual targeted resequencing studies.
SNP and indel calling for pooled and individual targeted resequencing studies.
VAAL
VAAL
A polymorphism discovery algorithm for short reads.
A polymorphism discovery algorithm for short reads.
VARiD
VARiD
A Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well…
A Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads.
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…
Vindel
Vindel
Detects redundant indels. Vindel, a simple yet effective computational pipeline, can be…
Detects redundant indels. Vindel, a simple yet effective computational pipeline, can be used to check whether a set of indels are redundant with respect to those already in the database of interest such as NCBI inverted question marks dbSNP. Of the…