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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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DeNovoGear
Desktop

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…

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Polymutt
Desktop

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…

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FamSeq
Desktop

FamSeq Family-based Sequencing program

A computational tool for calculating probability of variants in family-based…

A computational tool for calculating probability of variants in family-based sequencing data. It is still challenging to call rare variants. In family-based sequencing studies, information from all…

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denovolyzeR
Library

denovolyzeR

An integrated toolset for the analysis of de novo (sporadic) genetic sequence…

An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising…

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IsoMut
Desktop

IsoMut

Detects somatic mutations by considering all input samples and applying…

Detects somatic mutations by considering all input samples and applying filtering criteria at each genomic position. IsoMut is a robust method for calling unique mutations (SNVs and small indels)…

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mirTrios
Desktop
Web

mirTrios

Detects de novo mutations (DNMs) and rare inherited mutations from NGS data in…

Detects de novo mutations (DNMs) and rare inherited mutations from NGS data in sporadic diseases. The expectation-maximisation (EM) model was adopted to accurately identify DNMs from variant call…

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SeqHBase
Cloud

SeqHBase

A reliable big data-based computational toolset for efficiently manipulating…

A reliable big data-based computational toolset for efficiently manipulating genome-wide variants, annotations and every-site coverage in NGS studies. SeqHBase uses a heuristic framework of…

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TrioCaller
Desktop

TrioCaller

A linkage-disequilibrium framework to genotype inference in parents-offspring…

A linkage-disequilibrium framework to genotype inference in parents-offspring trios. TrioCaller will facilitate genotype calling and haplotype inference for many ongoing sequencing projects.

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TrioDeNovo
Desktop

TrioDeNovo

It is challenging to sift true mutations through massive amount of noise due to…

It is challenging to sift true mutations through massive amount of noise due to sequencing error and alignment artifacts. One of the critical limitations of existing methods is that for all genomic…

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DNMFilter
Desktop

DNMFilter De Novo Mutation Filter

A machine learning based tool designed to filter out false positive de novo…

A machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data. DNMFilter can be…

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