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Genome-wide association analysis software tools and databases

Genome-wide association studies (GWASs) have been heralded as a major advance in biomedical discovery, having identified ~2,000 robust associations with complex diseases since 2005.Source text:(Manolio, 2013) Bringing genome-wide association findings into clinical use. Nat Rev…

GWAS analysis steps

Experts in GWAS analysis

They share and annotate bioinformatics tools

Most recent bioinformatics tools

SuMu
Desktop

SuMu

Allows analysis of genetic data for association with phenotypes. SuMu is a…

Allows analysis of genetic data for association with phenotypes. SuMu is a package that allows users to study the link between genetic features and survival in the context of clinical data.

SNPhancers
Desktop

SNPhancers

Allows determination of the relationships between intergenic single nucleotide…

Allows determination of the relationships between intergenic single nucleotide polymorphisms (SNPs) as well as known enhancer regions in the human genome.

GenomicRobots
Desktop

GenomicRobots

Allows retrieval of genotypic information for sharing between collaborators.

Allows retrieval of genotypic information for sharing between collaborators.

PSST
Desktop

PSST Polygenic SNP Search Tool

Identifies multiple single nucleotide polymorphisms (SNPs) associated with…

Identifies multiple single nucleotide polymorphisms (SNPs) associated with diseases. PSST is a pipeline that allows: (1) identification modifying the penetrance of other SNPs, (2) assertion of…

Most popular analytical software and databases

PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on…

SKAT
Desktop

SKAT SNP-set (Sequence) Kernel Association Test

A SNP-set (e.g., a gene or a region) level test for association between a set…

A SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics…

PheWAS catalog
Dataset

PheWAS catalog

Contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs)…

Contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the…

i-GSEA4GWAS
Web

i-GSEA4GWAS improved GSEA for GWAS

A web-based resource for analysis of GWAS data to identify pathways/gene sets…

A web-based resource for analysis of GWAS data to identify pathways/gene sets correlated to certain traits by implementing an improved Gene Set Enrichment Analysis (i-GSEA) approach. i-GSEA4GWAS aims…

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