De Novo Mutation Filter
De Novo Mutation Filter
DNMFilter
A machine learning based tool designed to filter out false positive de novo mutations…
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 used as either a standalone tool to detect DNM or…
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…
denovolyzeR
denovolyzeR
An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants.…
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 in each human gene, from which one can infer the…
Family-based Sequencing program
Family-based Sequencing program
FamSeq
A computational tool for calculating probability of variants in family-based sequencing…
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 family members should be utilized to more…
mirTrios
mirTrios
Detects de novo mutations (DNMs) and rare inherited mutations from NGS data in sporadic…
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 files of a trio generated by GATK (Genome Analysis…
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…
SeqHBase
SeqHBase
A reliable big data-based computational toolset for efficiently manipulating genome-wide…
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 inheritance information for detecting de novo, inherited…
TrioCaller
TrioCaller
A linkage-disequilibrium framework to genotype inference in parents-offspring trios.…
A linkage-disequilibrium framework to genotype inference in parents-offspring trios. TrioCaller will facilitate genotype calling and haplotype inference for many ongoing sequencing projects.
TrioDeNovo
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 regions the same pre-specified mutation rate is…
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…