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Variant prioritization software tools | Whole-exome sequencing data analysis

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…
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VAAST
Desktop

VAAST Variant Annotation, Analysis and Search Tool

Identifies damaged genes and their disease-causing variants in personal genome…

Identifies damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of amino acid substitution (AAS) and aggregative approaches. The software can assay…

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eXtasy
Desktop
Web

eXtasy

A pipeline for ranking nonsynonymous single nucleotide variants given a…

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…

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KGGSeq
Desktop

KGGSeq

A three-level filtration and prioritization framework to identify the casual…

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…

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Phen-Gen
Desktop
Web

Phen-Gen

Combines patients' disease symptoms and sequencing data with prior domain…

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…

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MendelScan
Desktop

MendelScan

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

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

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CVE
Desktop

CVE Cancer Variant Explorer

Prioritizes variants to support genomics-driven decision-making. CVE can: (1)…

Prioritizes variants to support genomics-driven decision-making. CVE can: (1) annotate variant using Oncotator; (2) explore variant annotations; and (3) assess druggability using the Drug Gene…

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QueryOR
Web

QueryOR

Helps users to search genes. QueryOR combines different features in order to…

Helps users to search genes. QueryOR combines different features in order to make this platform easy to use. It works about the analysis of human variants from exome and genome sequencing. This tool…

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PhenIX
Web

PhenIX Phenotypic Interpretation of eXomes

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

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…

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cnvScan
Desktop

cnvScan

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

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…

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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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VCF.Filter
Desktop

VCF.Filter

Provides broad support for the VCF format, custom annotations, large VCF files,…

Provides broad support for the VCF format, custom annotations, large VCF files, and flexible analysis types. VCF.Filter is an easy-to-use, standalone, graphical software that allows the user to…

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PVP
Desktop

PVP PhenomeNET Variant Predictor

Allows highly accurate genome-scale identification of causative variants…

Allows highly accurate genome-scale identification of causative variants involved in human disease. PVP is a system which annotates and prioritizes disease variants in whole exome sequencing (WES)…

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VCF-Miner
Desktop

VCF-Miner

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

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…

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FILTUS
Desktop

FILTUS

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

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…

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PriVar
Desktop

PriVar

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

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…

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Variant Ranker
Web

Variant Ranker

Provides the ability to rank both coding and noncoding variants by encoding and…

Provides the ability to rank both coding and noncoding variants by encoding and integrating information from multiple sources. Variant Ranker is a web server for performing annotation, filtering and…

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BrowseVCF
Web
Desktop

BrowseVCF

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

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…

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Exomiser
Web

Exomiser

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

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

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UMD-Predictor
Web

UMD-Predictor

A computational combinatorial system to efficiently annotate cDNA substitutions…

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

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VarElect
Web

VarElect

A free web-based phenotype-dependent NGS variant prioritizer, which leverages…

A free web-based phenotype-dependent NGS variant prioritizer, which leverages the wealth of information in GeneCards and its affiliated databases. VarElect employs GeneCards’ powerful search and…

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Olorin
Desktop

Olorin

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

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…

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BiERapp
Web

BiERapp BioInformatic for Rare Diseases

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

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…

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OMIM Explorer
Web

OMIM Explorer

Allows rapid integration of phenotype with genotype to assist users in…

Allows rapid integration of phenotype with genotype to assist users in differential diagnostics of genetic disease, molecular variant prioritization, and novel gene-phenotype association discovery.…

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DriverPower
Desktop

DriverPower

Allows identification of coding and non-coding cancer drivers using mutational…

Allows identification of coding and non-coding cancer drivers using mutational burden and functional impact scores. DriverPower uses mutational burden and functional impact evidence to realize the…

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AVA,Dx
Desktop

AVA,Dx Analysis of Variation for Association with Disease

Utilizes whole exome sequencing data to detect Crohn’s disease (CD) status.…

Utilizes whole exome sequencing data to detect Crohn’s disease (CD) status. AVA,Dx is a disease-prediction model that assists users in research of undiscovered diseases. With this tool, researchers…

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ParamasivamEtAl…
Desktop

ParamasivamEtAl2017

Provides an analysis pipeline for detecting and classifying variants. The…

Provides an analysis pipeline for detecting and classifying variants. The algorithm allows computing data from whole exome sequencing (WES) and whole genome sequencing (WGS) from trios or larger…

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Episcore
Algorithm

Episcore

Predicts haploinsufficiency (HIS) using epigenomic features and Random Forest…

Predicts haploinsufficiency (HIS) using epigenomic features and Random Forest method. Episcore provides complementary information to mutation intolerance metrics. It enables applications of…

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GARFIELD-NGS
Desktop

GARFIELD-NGS Genomic vARiants FIltering by dEep Learning moDels in NGS

Classifies true and false variants. GARFIELD-NGS can be applied in single…

Classifies true and false variants. GARFIELD-NGS can be applied in single sample whole exome sequencing (WES) analysis and it is effective on single nucleotide polymorphisms (SNPs) and…

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VCF-Explorer
Desktop

VCF-Explorer

Provides a powerful alternative environment for whole genome studies.…

Provides a powerful alternative environment for whole genome studies. VCF-Explorer is a software tool which is designed to carry out analysis for large VCF files. It is lightweight in structure and…

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GeMSTONE
Web

GeMSTONE Germline Mutation Scoring Tool fOr Next-Generation sEquencing data

Allows an accessible, collaborative, replicable and holistic analysis of…

Allows an accessible, collaborative, replicable and holistic analysis of genetic variants. GeMSTONE permits to eliminate the time and space burdens associated with modern variant analysis tools. It…

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MARRVEL
Dataset

MARRVEL Model organism Aggregated Resources for Rare Variant ExpLoration

Contains information from six human genetic databases and seven model organism…

Contains information from six human genetic databases and seven model organism databases. MARRVEL is able to provide a concise summary regarding the human gene homologs in budding and fission yeast,…

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HIPred
Desktop

HIPred

Integrates genomic and evolutionary information from ENSEMBL, with functional…

Integrates genomic and evolutionary information from ENSEMBL, with functional annotations from ENCODE consortium and the NIH Roadmap Epigenomics Project to predict haploinsufficiency. HIPred is a…

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mirVAFC
Web

mirVAFC

Serves for pathogenic sequence variants prioritizations according to the ACMG…

Serves for pathogenic sequence variants prioritizations according to the ACMG guidelines. The mirVAFC webserver is developed for clinical exome sequencing (CES) variants data analysis for single…

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RETA
Desktop

RETA

Provides a one-stop analysis of these data and a comprehensive, interactive and…

Provides a one-stop analysis of these data and a comprehensive, interactive and easy-to-understand report with many advanced visualization features. RETA is an R package that includes various…

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OVA
Web

OVA Ontology Variant Analysis

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

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…

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GeneCOST
Desktop

GeneCOST

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

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.…

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HetRank
Desktop

HetRank

A flexible gene-ranking method that incorporates interaction network data.…

A flexible gene-ranking method that incorporates interaction network data. HetRank consistently prioritizes more disease-causing genes than existing analysis methods. It addresses the problem of…

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wKGGSeq
Web

wKGGSeq

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

A user-friendly online framework, wKGGSeq, to provide systematic annotation, filtration, prioritization, and visualization functions for characterizing causal mutation(s) in exome sequencing studies…

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SPRING
Desktop
Web

SPRING Snv PRioritization via the INtegration of Genomic data

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

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…

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Varapp
Web
Desktop

Varapp

An open-source web application to filter variants from large sets of exome data…

An open-source web application to filter variants from large sets of exome data stored in a relational database. Varapp implements different scenarios for Mendelian diseases (dominant, recessive, de…

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ContrastRank
Web

ContrastRank

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

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…

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ExomeWalker
Web

ExomeWalker

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

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)…

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Mendelian
Desktop

Mendelian

Permits analysis of several types of variants, including single nucleotide…

Permits analysis of several types of variants, including single nucleotide polymorphisms (SNPs), insertion-deletions (indels) and structural variants (SV). Mendelian was tested by reanalyzing the…

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VaRank
Desktop

VaRank

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

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…

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VarSifter
Desktop

VarSifter

A graphical software tool for desktop computers that allows investigators of…

A graphical software tool for desktop computers that allows investigators of varying computational skills to easily and quickly sort, filter, and sift through sequence variation data.

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exomeSuite
Desktop

exomeSuite

Analyzes variant calls from multiple individuals to facilitate identification…

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…

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VAR-MD
Desktop

VAR-MD

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

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,…

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Glints
Web

Glints GLobal INference of disease-causing varian TS

Identifies disease-causing Single Nucleotide Variants (SNVs) in both coding and…

Identifies disease-causing Single Nucleotide Variants (SNVs) in both coding and flanking noncoding regions from exome sequencing data. Glints respects the query disease in exome sequencing studies to…

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IndelPrioritize…
Desktop

IndelPrioritizer

Prioritizes indels from exome sequencing data by integrating phenotype…

Prioritizes indels from exome sequencing data by integrating phenotype information and functional effect predictions. IndelPrioritizer integrates five functional prediction scores, four genic…

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