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De novo mutation detection software tools | Whole-genome sequencing data analysis

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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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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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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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Mendel,MD
Web
Desktop

Mendel,MD

Organizes, annotates, filters and diagnoses patients with Mendelian Disorders…

Organizes, annotates, filters and diagnoses patients with Mendelian Disorders using Exome and Genome sequencing data or experimental validation and possible diagnosis. Mendel,MD combines several…

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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
Desktop

denovolyzeR

Provides tools for the analysis of de novo coding sequence variants.…

Provides tools for the analysis of de novo coding sequence variants. denovolyzeR is an R implementation of a statistical framework for the analysis of de novo genetic variants. It estimates the…

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TrioDeNovo
Desktop

TrioDeNovo

Evaluates evidence of de novo mutation (DNM) mainly based on the data and…

Evaluates evidence of de novo mutation (DNM) mainly based on the data and adjusts post-hoc the effect of mutation rates on the calling through prior odds. TrioDeNovo is applicable to exome sequencing…

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mirTrios
Web
Desktop

mirTrios

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

Detects de novo mutations (DNMs) and rare inherited mutations from next-generation sequencing (NGS) data in sporadic diseases. mirTrios can be employed in the identification of rare inherited…

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SeqHBase
Desktop

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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DNMFilter
Desktop

DNMFilter De Novo Mutation Filter

Classifies candidates as true or false de novo mutations. DNMFilter uses…

Classifies candidates as true or false de novo mutations. DNMFilter uses gradient boosting as the classification algorithm to filter De Novo Mutations (DNMs) identified in parent–offspring trios.…

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forestDNM
Desktop

forestDNM

Automates the discovery of de novo single-nucleotide variant (SNV) mutations…

Automates the discovery of de novo single-nucleotide variant (SNV) mutations (DNMs) from family genotype data (provided in a VCF). forestDNM is an R package with a command-line executable. It use a…

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