GWAS Bioinformatics MCP Server

by zaeyasa·io.github.zaeyasa/gwas-mcp·v1.0.2·1 stars

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Access 30+ bioinformatics tools from 14 databases.

B75/100grade B

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B75/100

full report

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1 stars47 downloads/wk

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GWAS Bioinformatics MCP Server tools (44, 5 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

annotate_snps
Annotate SNPs with gene names, functional consequences, and allele frequencies from Ensembl VEP and gnomAD.
calculate_genomic_inflation
Calculate genomic inflation factor (lambda GC) from GWAS summary statistics. Used to assess population stratification.
calculate_heritability_ldsc
Estimate SNP-heritability using LD Score regression. Requires GWAS summary statistics and LD scores.
calculate_missingness
Calculate per-individual and per-variant missingness rates from genotype data.
calculate_pca
Perform Principal Component Analysis for population stratification. Uses PLINK files as input.
calculate_prs
Calculate Polygenic Risk Scores (PRS) for individuals using GWAS summary statistics and target genotypes.
clump_snps
Perform LD-based clumping of GWAS results to identify independent significant signals.
create_manhattan_plotwrite action
Create a Manhattan plot from GWAS summary statistics. Shows -log10(p-value) across chromosomes.
create_pca_plotwrite action
Create a PCA scatter plot showing population structure. Plots PC1 vs PC2.
create_qq_plotwrite action
Create a Quantile-Quantile (QQ) plot from GWAS p-values. Shows observed vs expected p-values.
create_regional_plotwrite action
Create a regional association plot (LocusZoom-style) for a specific genomic region around a lead SNP.
extract_locus
Extract genotype data for a specific genomic region around a lead SNP for fine-mapping.
gene_set_enrichment
Perform gene set enrichment analysis using GO and KEGG pathways via Enrichr.
get_alphafold_structure
Get AlphaFold AI-predicted protein structure by UniProt ID. Returns structure confidence and download links.
get_clinvar_variant
Get detailed ClinVar information for a specific variant by rsID or ClinVar ID.
get_disease_associations
Get disease associations for a gene from Open Targets with evidence scores.
get_drug_gene_interactions
Get drug-gene interaction annotations from PharmGKB for a specific gene.
get_drug_targets
Get drug target information from Open Targets for a gene. Shows drugs in development and approved drugs targeting this gene.
get_eqtl_data
Get expression quantitative trait loci (eQTL) data from GTEx for a SNP and tissue.
get_functional_enrichment
Get functional enrichment analysis for a list of proteins using STRING. Returns enriched GO terms, pathways, and domains.
get_gene_diseases
Get genetic diseases associated with a gene from OMIM and other sources.
get_gene_pathways
Find all KEGG pathways that a gene participates in.
get_interaction_network
Get interaction network between a list of proteins from STRING. Shows how multiple proteins interact with each other.
get_interpro_domains
Get protein domain information from InterPro for a given UniProt ID or protein sequence.
get_kegg_pathway
Get detailed KEGG pathway information including genes and description.
get_pdb_structure
Get detailed information about a PDB structure by PDB ID.
get_protein_details
Get detailed protein information from UniProt by UniProt accession ID. Returns full protein details including function, domains, and GO annotations.
get_protein_interactions
Get protein-protein interaction network from STRING database. Shows what proteins interact with your protein of interest.
get_variant_info
Get detailed variant/SNP information from Ensembl by rsID. Returns position, alleles, clinical significance, and consequences.
identify_significant_snps
Filter GWAS results to identify genome-wide significant SNPs based on p-value threshold.
ld_pruning
Prune SNPs based on linkage disequilibrium (LD). Removes variants in high LD to create an independent set.
query_gwas_catalog
Query the NHGRI-EBI GWAS Catalog for previously reported associations for a SNP or trait.
run_gwaswrite action
Perform genome-wide association study using linear or logistic regression. Returns summary statistics including p-values, beta coefficients, and standard errors.
search_alphafold
Search AlphaFold database for predicted structures by gene name or protein name.
search_clinvar
Search ClinVar for clinical variant interpretations. Find pathogenic/benign classifications for genetic variants.
search_ensembl_gene
Search Ensembl for gene information by gene symbol or Ensembl ID. Returns gene location, biotype, and description.
search_kegg_pathway
Search KEGG for metabolic and signaling pathways by name or gene.
search_ncbi_gene
Search NCBI Gene database for gene information by gene symbol, name, or ID.
search_omim
Search OMIM (Online Mendelian Inheritance in Man) for genetic diseases and phenotypes.
search_open_targets
Search Open Targets Platform for genes, diseases, or drugs.
search_pdb_structures
Search PDB for protein 3D structures by protein name, gene name, or UniProt ID.
search_pharmgkb
Search PharmGKB for drug-gene interactions and pharmacogenomics data.
search_uniprot
Search UniProt for protein information by protein name, gene name, or UniProt ID. Returns protein function, sequence info, and associated genes.
vcf_quality_check
Perform quality control on a VCF file. Filters variants based on MAF, missingness, and Hardy-Weinberg equilibrium.

Public scan report

scanner v0.1.10 · 2026-09-28 · same rubric, same numbers if you re-run it

no findings

Code scan18 source files scanned25/25
–Live reliabilityno gateway calls yet and no remote to proben/a
–Tool poisoningtools not inspected (local package is not executed); not countedn/a
Auth qualitylocal package, no credentials required12/15
Maintenancelast push 231 days ago4/15
Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10

Overall 75/100. Components that don't apply are left out of the denominator. Any critical finding is an F.Rubric Appeal a finding JSON

How GWAS Bioinformatics MCP Server compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score: 75/100; higher than 45% of 48,255 servers
Tools: 44; the typical server has 7
Tools that change things: 11%; typical: 0%. Fewer write tools means less an agent can break
GitHub stars: 1; more than 65% of 28,688 servers
Downloads a week: 47; more than 39% of 12,191 servers with a package

What its tools let an agent do: 39 read · 4 create · 1 run or deploy

Install GWAS Bioinformatics MCP Server in Claude Code, Cursor or VS Code

claude mcp add gwas-mcp -- uvx gwas-mcp

Add to Cursor

What the publisher says

From the GWAS Bioinformatics MCP Server repository's README, as published. We do not edit it. Read it on GitHub

🧬 GWAS-MCP: Bioinformatics MCP Server

A powerful Model Context Protocol (MCP) server for GWAS and bioinformatics research. Seamlessly integrates with Claude Desktop and other MCP clients to provide AI-powered access to major biological databases.

✨ Features

🔬 Protein & Gene Lookup

UniProt - Search proteins by name, gene, or ID
Ensembl - Gene information and variant details
NCBI Gene - Comprehensive gene database

🧪 Clinical & Variants

ClinVar - Clinical variant interpretations (pathogenic/benign)
GWAS Catalog - Genome-wide association studies
GTEx - Expression quantitative trait loci (eQTL)

🔗 Protein Interactions & Networks

STRING - Protein-protein interactions
InterPro - Protein domains and families

🏗️ Structures & Pathways

AlphaFold - AI-predicted protein structures
PDB - Experimental 3D structures
KEGG - Metabolic and signaling pathways

💊 Drug Discovery

Open Targets - Drug target validation & disease associations
PharmGKB - Pharmacogenomics & drug-gene interactions

🏥 Genetic Diseases

OMIM - Online Mendelian Inheritance in Man

🚀 Quick Start

Installation

pip install gwas-mcp

Claude Desktop Configuration

Add to your claudedesktopconfig.json:

{
  "mcpServers": {
    "gwas-bioinformatics": {
      "command": "python",
      "args": ["-m", "gwas_mcp.server"]
    }
  }
}

Config file location:

Windows: %APPDATA%\Claude\claudedesktopconfig.json
macOS: ~/Library/Application Support/Claude/claudedesktopconfig.json
Linux: ~/.config/Claude/claudedesktopconfig.json

Restart Claude Desktop

After adding the configuration, restart Claude Desktop to load the MCP server.

🛠️ Available Tools

Protein & Gene Tools

Clinical & Variant Tools

Protein Interaction Tools

Structure & Pathway Tools

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

GWAS Bioinformatics MCP Server: common questions

Is GWAS Bioinformatics MCP Server safe?: Mostly: it is graded B (75/100). Read the GWAS Bioinformatics MCP Server safety report
How do I install GWAS Bioinformatics MCP Server?: It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does GWAS Bioinformatics MCP Server need an API key?: Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is GWAS Bioinformatics MCP Server maintained?: The last commit was 267 days ago (2026-02-09). The latest release is v1.0.2.
How does GWAS Bioinformatics MCP Server compare with other MCP servers?: safety score 75/100 (higher than 45% of 48,255 servers); tools 44 (the typical server has 7); tools that change things 11% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.