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Variant prioritization software tools | Whole-exome sequencing

High-throughput sequencing software tools > Whole-exome sequencing software tools

Whole-exome sequencing has become a fundamental tool for the discovery of disease-related genes of familial diseases and the identification of somatic driver variants in cancer. However, finding the causal mutation among the enormous background of individual variability in a small number of samples is still a big challenge. Source text: Aleman et al., 2014.

BioInformatic for Rare Diseases

OMIC_05449

BioInformatic for Rare Diseases
BiERapp

Helps in the identification of causative variants in family and sporadic genetic…

Helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies,…

BrowseVCF

OMIC_10905

BrowseVCF

Enables researchers to browse, query and filter millions of variants in a few seconds.…

Enables researchers to browse, query and filter millions of variants in a few seconds. Top features include the possibility to store intermediate search results, to query user-defined gene lists, to group samples for family or tumour/normal studies,…

cnvScan

OMIC_11023

cnvScan

A tool to improve the clinical utility of computational CNV prediction in exome data.…

A tool to improve the clinical utility of computational CNV prediction in exome data. cnvScan can accept input from any CNV prediction program. cnvScan consists of two steps: CNV screening and CNV annotation. CNV screening evaluates CNV prediction…

ContrastRank

OMIC_09789

ContrastRank

A method for prioritizing putative impaired genes in cancer. ContrastRank is based on the…

A method for prioritizing putative impaired genes in cancer. ContrastRank is based on the comparison of exome sequencing data from different cohorts and can detect putative cancer driver genes. The method can also be used to estimate a global score…

exomeSuite

OMIC_04839

exomeSuite

Analyzes variant calls from multiple individuals to facilitate identification of causal…

Analyzes variant calls from multiple individuals to facilitate identification of causal mutations. exomeSuite filters for putative causative variants of monogenic diseases inherited in one of three forms: dominant, recessive caused by a homozygous…

ExomeWalker

OMIC_07804

ExomeWalker

A computational method to prioritize a set of candidates in exome sequencing projects…

A computational method to prioritize a set of candidates in exome sequencing projects that aim to identify novel Mendelian disease genes. This approach involves filtering a Variant Call Format (VCF) file according to a number of user-definable…

Exomiser

OMIC_05448

Exomiser

A Java program that functionally annotates variants from whole-exome sequencing data…

A Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file.

eXtasy

OMIC_00150

eXtasy

A pipeline for ranking nonsynonymous single nucleotide variants given a specific…

A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype. eXtasy takes into account the putative deleteriousness of the variant, haploinsufficiency predictions of the underlying gene and the similarity of the given…

FILTUS

OMIC_11098

FILTUS

A standalone tool for working with annotated variant files, e.g. when searching for…

A standalone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. Very flexible in terms of input file formats, FILTUS offers efficient filtering and a range of downstream utilities, including…

GeneCOST

OMIC_09390

GeneCOST

A scoring based method to evaluate every gene for their disease association. GeneCOST has…

A scoring based method to evaluate every gene for their disease association. GeneCOST has major advantages over existing programs. GeneCOST supports pedigree information and multiple patient cases. The program does not require any prior knowledge of…

KGGSeq

OMIC_02260

KGGSeq

A three-level filtration and prioritization framework to identify the casual mutation(s)…

A three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate…

MendelScan

OMIC_00065

MendelScan

Variant scoring and linkage mapping for family exome sequencing. MendelScan is a tool for…

Variant scoring and linkage mapping for family exome sequencing. MendelScan is a tool for prioritizing candidate variants in family-based studies of inherited disease.

Olorin

OMIC_01556

Olorin

An interactive filtering tool for next generation sequencing data coming from the study…

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively…

OMIM Explorer

OMIC_11207

OMIM Explorer

Provides rapid integration of phenotype with genotype to aid in differential diagnostics…

Provides rapid integration of phenotype with genotype to aid in differential diagnostics of genetic disease, molecular variant prioritization, and novel gene-phenotype association discovery. OMIM Explorer extends the biomedical application of…

Ontology Variant Analysis

OMIC_09625

Ontology Variant Analysis
OVA

A variant prioritization tool in which user-provided phenotypic information is exploited…

A variant prioritization tool in which user-provided phenotypic information is exploited to infer deeper biological context. OVA combines a knowledge-based approach with a variant-filtering framework. It reduces the number of candidate variants by…

Phen-Gen

OMIC_09741

Phen-Gen

Combines patients’ disease symptoms and sequencing data with prior domain knowledge…

Combines patients’ disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders. Simulations revealed that the causal variant was ranked first in 88% of cases when it was a coding variant-a…

Phenotypic Interpretation of eXomes

OMIC_09742

Phenotypic Interpretation of eXomes
PhenIX

A pipeline for ranking (prioritizing) candidate genes in exomes or NGS panels with…

A pipeline for ranking (prioritizing) candidate genes in exomes or NGS panels with comprehensive coverage of human Mendelian disease genes. PhenIX ranks genes based on predicted variant pathogenicity as well as phenotypic similarity of diseases…

PriVar

OMIC_00160

PriVar

A cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from…

A cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and information of external databases. PriVar contains four modules: annotation,…

Snv PRioritization via the INtegration of Genomic…

OMIC_07796

Snv PRioritization via the INtegration of Genomic data
SPRING

A bioinformatics method for the prediction of disease-causing nonsynonymous single…

A bioinformatics method for the prediction of disease-causing nonsynonymous single nucleotide variants (SNVs) in exome sequencing studies. Given a query disease and a set of candidate nonsynonymous SNVs, SPRING calculates a q-value to indicate the…

UMD-Predictor

OMIC_11209

UMD-Predictor

A computational combinatorial system to efficiently annotate cDNA substitutions of all…

A computational combinatorial system to efficiently annotate cDNA substitutions of all human transcripts for their potential pathogenicity. UMD-Predictor combines biochemical properties, impact on splicing signals, localization in protein domains,…

VAR-MD

OMIC_09391

VAR-MD

A software tool for analyzing the DNA sequence variants produced by human ES. VAR-MD…

A software tool for analyzing the DNA sequence variants produced by human ES. VAR-MD generates a ranked list of variants using predicted pathogenicity, Mendelian inheritance models, genotype quality, and population variant frequency data. VAR-MD has…

VaRank

OMIC_10061

VaRank

A simple and powerful tool designed for variant ranking from next generation sequencing…

A simple and powerful tool designed for variant ranking from next generation sequencing data. VaRank provides a comprehensive workflow for annotating and ranking SNVs and indels. Four modules create the strength of this workflow: – Variant call…

Variant Annotation, Analysis and Search Tool

OMIC_02134

Variant Annotation, Analysis and Search Tool
VAAST

A probabilistic search tool for identifying damaged genes and their disease-causing…

A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing phylogenetic conservation, amino acid substitution (AAS) and aggregative approaches to variant…

VCF-Miner

OMIC_10906

VCF-Miner

A graphical user interface for sorting, filtering and querying information encoded in VCF…

A graphical user interface for sorting, filtering and querying information encoded in VCF files. Powered by a MongoDB database engine, VCF-Miner enables the stepwise trimming of non-relevant variants. The grouping feature implemented in VCF-Miner…

wKGGSeq

OMIC_09389

wKGGSeq

A user-friendly online framework, wKGGSeq, to provide systematic annotation, filtration,…

A user-friendly online framework, wKGGSeq, to provide systematic annotation, filtration, prioritization, and visualization functions for characterizing causal mutation(s) in exome sequencing studies of inherited disorders. wKGGSeq provides: (1) a…

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