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Indel detection software tools | Pool sequencing data analysis

Pooled-DNA sequencing strategies enable fast, accurate, and cost-effect detection of rare variants, but current approaches are not able to accurately identify short insertions and deletions (indels), despite their pivotal role in genetic disease.…
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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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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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Syzygy
Desktop

Syzygy

SNP and indel calling for pooled and individual targeted resequencing studies.

SNP and indel calling for pooled and individual targeted resequencing studies.

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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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Dindel
Desktop

Dindel

A Bayesian method to call indels from short-read sequence data in individuals…

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…

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SPLINTER
Desktop
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vipR
Desktop

vipR

A program to screen for sequence variants (SNPs, deletions) in sequence data…

A program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

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FreeBayes
Desktop

FreeBayes

A Bayesian genetic variant detector designed to find small polymorphisms,…

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.

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