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SNP prioritization software tools | Genome-wide association analysis

Although there are millions of SNPs deposited in public SNP databases, only a small proportion of them are functional polymorphisms that contribute to disease phenotypes. Thus, prioritizing SNPs based on their phenotypic risks is essential for…
SNPrank
Desktop

SNPrank

Classifies single nucleotide polymorphisms (SNPs) according to a genetic…

Classifies single nucleotide polymorphisms (SNPs) according to a genetic association interaction network. SNPrank supplies a network-based approach to detect important hub SNPs through conditional…

Gentrepid
Web

Gentrepid

Identifies candidates based on shared biomolecular pathways or domain-based…

Identifies candidates based on shared biomolecular pathways or domain-based protein homology. Gentrepid is based on combined bioinformatics approach including methods of domain comparison and protein…

MiSPU
Desktop

MiSPU Microbiome-based Sum of powered score

Allows users to test overall association between a microbial community and an…

Allows users to test overall association between a microbial community and an outcome of interest. MisPU is a method, inspired by the aSPU test that introduces the variable of generalized taxon…

SNPinfo
Web

SNPinfo

Provides a toolkit for organize, annotate, and select single nucleotide…

Provides a toolkit for organize, annotate, and select single nucleotide polymorphisms (SNPs). SNPinfo is composed of three pipelines and three additional tools. The platform can be used for either…

VEXOR
Web

VEXOR

Intends to characterize the functional context in fine-mapping analyses of…

Intends to characterize the functional context in fine-mapping analyses of complex traits. VEXOR enables to visualize, explore and interpret outputs generated by genome-wide genotyping arrays (GWAS)…

HaploReg
Web

HaploReg

A tool for exploring annotations of the noncoding genome at variants on…

A tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes…

SPOT
Web

SPOT SNP Prioritization Online Tool

A web site for integrating biological databases into the prioritization of…

A web site for integrating biological databases into the prioritization of single nucleotide polymorphisms (SNPs) for further study after a genome-wide association study (GWAS). Typically, the next…

VSE
Desktop

VSE Variant Set Enrichment

Calculates the enrichment of a set of disease-associated variants across…

Calculates the enrichment of a set of disease-associated variants across functionally annotated genomic regions, consequently highlighting the mechanisms important in the etiology of the disease…

PPFS
Desktop

PPFS Predict Phenotypes From SNPs

Recognizes single nucleotide polymorphisms (SNPs) that are non-randomly…

Recognizes single nucleotide polymorphisms (SNPs) that are non-randomly associated with a phenotype. PPFS allows users to select the approximate fraction of strains to include in their subset. It…

MetaRanker
Web

MetaRanker

Prioritizes the protein-coding part of the human genome to shortlist candidate…

Prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 allows user to upload lists of genes and their scores, which can…

RolyPoly
Desktop

RolyPoly

Uses enrichment of genome-wide association summary statistics to identify…

Uses enrichment of genome-wide association summary statistics to identify trait-relevant cellular functional annotations. RolyPoly is a regression-based polygenic model that can prioritize…

regSNPs‑splic…
Web

regSNPs‑splicing

Prioritizes deleterious synonymous single-nucleotide variants (sSNVs).…

Prioritizes deleterious synonymous single-nucleotide variants (sSNVs). regSNPs-splicing shows good results when using pathogenic variants contain substantial number of variants. It includes protein…

PhenoPred
Web

PhenoPred

Detects novel gene-disease associations in humans. PhenoPred is based on an…

Detects novel gene-disease associations in humans. PhenoPred is based on an experimental protein-protein interaction (PPI) network, protein-disease associations, as well as protein sequence and…

FastTagger
Desktop

FastTagger

Allows to work on genome-wide tag single nucleotide polymorphisms (SNP)…

Allows to work on genome-wide tag single nucleotide polymorphisms (SNP) selection using multi-marker linkage disequilibrium (LD). FastTagger uses several techniques to reduce running time and memory…

FunciSNP
Desktop

FunciSNP

Enables the identification of candidate functional SNPs by integrating…

Enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which…

iGWAS
Desktop

iGWAS integrative Genome-Wide Association Studies

Analyzes multiplatform genomic data under the family-based design. The iGWAS…

Analyzes multiplatform genomic data under the family-based design. The iGWAS approach is developed within the framework of causal mediation modeling using counterfactuals. It considers the…

GARFIELD
Desktop
GenoWAP
Desktop

GenoWAP

A post-GWAS prioritization method that integrates genomic functional annotation…

A post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. After prioritization, real disease-associated loci become easier to be identified. Within…

fgwas
Desktop

fgwas

A command line tool for integrating functional genomic information into a…

A command line tool for integrating functional genomic information into a genome-wide association study (GWAS). The basic setup is as follows: you have performed a GWAS or a meta-analysis of many…

GenoSkyline
Desktop

GenoSkyline

An unsupervised learning framework to predict tissue-specific functional…

An unsupervised learning framework to predict tissue-specific functional regions through integrating high-throughput epigenomic annotations. GenoSkyline successfully identified a variety of…

G T A T C G C T A
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…

CBSD_Trancriptomics
Desktop

CBSD_Trancriptomics Cassava Brown Streak Disease Trancriptomics

Provides scripts for Cassava Brown Streak Disease analyses. CBSD_Trancriptomics…

Provides scripts for Cassava Brown Streak Disease analyses. CBSD_Trancriptomics provides single and multi-kernel Genomic Best Linear Unbiased Predictions (GBLUP) models with markers imputed to whole…

DeepWAS
Desktop

DeepWAS

Allows detection of individual regulatory single nucleotide polymorphisms…

Allows detection of individual regulatory single nucleotide polymorphisms (SNPs) from genotypes. DeepWAS proceeds to identification of individual regulatory SNPs by investigating genomic location and…

ReMo-SNPs
Desktop

ReMo-SNPs

Allows users to search polymorphic markers in specified regions and/or motifs…

Allows users to search polymorphic markers in specified regions and/or motifs genome-wide. ReMo-SNPs can analyze genome-wide data and combine input from in silico and in vitro analyses. The software…

LiuEtAl2017
Algorithm

LiuEtAl2017

Identifies possibly functional transcription factors (TFs) in breast…

Identifies possibly functional transcription factors (TFs) in breast cancer-relevant cells by using data from open chromatin genomic data and gene expression. The method first detects Genome-wide…

SiNoPsis
Web

SiNoPsis

Characterizes single nucleotide polymorphisms (SNPs) in the context of known…

Characterizes single nucleotide polymorphisms (SNPs) in the context of known annotated human genes or a region defined by genomic coordinates. SiNoPsis presents candidate SNPs related to the…

PhosphoPICK-SNP
Web

PhosphoPICK-SNP

Allows researchers to submit protein sequences and amino acid variants in the…

Allows researchers to submit protein sequences and amino acid variants in the protein. PhosphoPICK-SNP is a web application that permits to analyze non-synonymous single nucleotide variants (nsSNVs)…

FUMA
Web

FUMA Functional Mapping and Annotation

Provides an easy-to-use tool to functionally annotate, visualize, and…

Provides an easy-to-use tool to functionally annotate, visualize, and interprets results from genetic association studies and to quickly gain insight into the directional biological implications of…

MinorityReport
Desktop

MinorityReport

Facilitates the comparison of any two sets of genome alignments for the purpose…

Facilitates the comparison of any two sets of genome alignments for the purpose of rapidly identifying the spectrum of nonsynonymous changes, insertions or deletions. MinoritReport also copies number…

motifbreakR
Desktop

motifbreakR

An R package for predicting the disruptiveness of single nucleotide…

An R package for predicting the disruptiveness of single nucleotide polymorphisms on transcription factor binding sites. motifbreakR allows the biologist to judge whether the sequence surrounding a…

Enlight
Web

Enlight

Draws regional plots for GWAS results, and overlays epigenetic modification,…

Draws regional plots for GWAS results, and overlays epigenetic modification, DNase sensitivity site, transcription factor binding annotation, eQTL information, HiC-seq interaction onto it. The…

GREGOR
Desktop

GREGOR Genomic Regulatory Elements and Gwas Overlap algoRithm

A tool to test for enrichment of an input list of trait-associated index SNPs…

A tool to test for enrichment of an input list of trait-associated index SNPs in experimentally annotated regulatory domains (BED files). GREGOR systematically evaluates enrichment of genetic…

VASP
Desktop

VASP Variant Analysis of Sequenced Pedigrees

A flexible data integration environment capable of producing a summary of…

A flexible data integration environment capable of producing a summary of pedigree variation, providing relevant information such as compound heterozygosity, genome phasing and disease inheritance…

SNPsnap
Web

SNPsnap

Enables SNP-based enrichment analysis by providing matched sets of SNPs that…

Enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap efficiently identifies sets of randomly drawn SNPs…

RegulomeDB
Web

RegulomeDB

A database that annotates SNPs with known and predicted regulatory elements in…

A database that annotates SNPs with known and predicted regulatory elements in the intergenic regions of the H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase…

FitSNPs
Desktop
Web

FitSNPs

Candidate single nucleotide polymorphisms (SNPs) from genome-wide association…

Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased.…

GPA
Desktop

GPA Genetic analysis incorporating Pleiotropy and Annotation

A statistical approach to prioritizing GWAS results by integrating pleiotropy…

A statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data. 'GPA' package provides computationally efficient and user friendly interface…

GWAS3D
Web

GWAS3D

A web server to systematically analyze the genetic variants that could affect…

A web server to systematically analyze the genetic variants that could affect regulatory elements, by integrating annotations from cell type-specific chromatin states, epigenetic modifications,…

PupaSuite
Web

PupaSuite

An interactive web-based SNP analysis tool that allows for the selection of…

An interactive web-based SNP analysis tool that allows for the selection of relevant SNPs within a gene, based on different characteristics of the SNP itself, such as validation status, type,…

HapTagger
Desktop

HapTagger

Allows to find tag single-nucleotide polymorphism (SNPs) thanks to multimarker…

Allows to find tag single-nucleotide polymorphism (SNPs) thanks to multimarker haplotypes. HapTagger integrates several algorithms which serve to select tag SNPs and to solve the subproblems. This…

SNPranker
Web

SNPranker

A bioinformatics approach to support biological data mining in the analysis and…

A bioinformatics approach to support biological data mining in the analysis and interpretation of SNPs associated to pathologies. A user-friendly interface allows the input of a list of genes, SNPs…

LDassoc
Web

LDassoc

Allows exploration of genome-wide association studies (GWAS) association…

Allows exploration of genome-wide association studies (GWAS) association results. LDassoc is a web module, in the LDlink suite of web tools, allowing users to upload and visualize GWAS association…

vcfsubsample
Desktop

vcfsubsample

Helps about the Genome Wide Association (GWA) studies problem. Vcfsubsample…

Helps about the Genome Wide Association (GWA) studies problem. Vcfsubsample subsamples the data in order to "lock" the minor allele frequency (MAF) in the data set, i.e. all single…

snvForest
Desktop
Web
FastSNP
Web

FastSNP Function Analysis and Selection Tool for Single Nucleotide Polymorphisms

Allows users to efficiently identify and prioritize high-risk SNPs according to…

Allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect…

FESTA
Desktop

FESTA Fragmented Exhaustive Search for TAgging SNPs

Implements efficient algorithms for tagging single nucleotide polymorphism…

Implements efficient algorithms for tagging single nucleotide polymorphism (tagSNP) selection based on pairwise linkage disequilibrium (LD) measure r2. FESTA allows to realize an exhaustive search…

Gene Prospector
Web

Gene Prospector

Helps researchers to prioritize and evaluate evidence for genes related to…

Helps researchers to prioritize and evaluate evidence for genes related to human disease or interactions with non-genetic risk factors. Gene Prospector provides supporting evidence derived from a…

ASSIMILATOR
Desktop

ASSIMILATOR

Compares experimental evidence available for single nucleotide polymorphisms…

Compares experimental evidence available for single nucleotide polymorphisms (SNPs) to identify those which can be functionally important. ASSIMILATOR queries information about SNPs from the UCSC…

SYSNPs
Web

SYSNPs Select Your SNPs

Allows compilation of information about all the single nucleotide polymorphisms…

Allows compilation of information about all the single nucleotide polymorphisms (SNPs) in any set of human genes or genome regions of interest. SYSNPs allows users to select some of them by different…

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