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GWAS Bioinformatics MCP Server

Access 30+ bioinformatics tools from 14 databases.

Connector by zaeyasa · GitHub account verified by the MCP Registry

IndexedMITLocal (stdio)★ 1
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Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/zaeyasa-gwas-mcp

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About

Access 30+ bioinformatics tools from 14 databases.

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Permissions

What this server can do and what it asks for, from its tool list and install config. Checked Oct 25, 2026.

Tools
35 read · 6 write · 1 delete · 2 not yet classified
Secrets
None asked for
Install scripts
Not scanned yet
Runs as
Python package

Tools by what they do 44

Read from the source code; the running server may list different tools.

Read 35 · Look things up without changing anything.

  • calculate_genomic_inflation
  • calculate_heritability_ldsc
  • calculate_missingness
  • calculate_pca
  • calculate_prs
  • extract_locus
  • get_alphafold_structure
  • get_clinvar_variant
  • get_disease_associations
  • get_drug_gene_interactions
  • get_drug_targets
  • get_eqtl_data
Show 23 more tools
  • get_functional_enrichment
  • get_gene_diseases
  • get_gene_pathways
  • get_interaction_network
  • get_interpro_domains
  • get_kegg_pathway
  • get_pdb_structure
  • get_protein_details
  • get_protein_interactions
  • get_variant_info
  • identify_significant_snps
  • query_gwas_catalog
  • search_alphafold
  • search_clinvar
  • search_ensembl_gene
  • search_kegg_pathway
  • search_ncbi_gene
  • search_omim
  • search_open_targets
  • search_pdb_structures
  • search_pharmgkb
  • search_uniprot
  • vcf_quality_check

Write 6 · Create, change, send or run things.

  • create_manhattan_plot
  • create_pca_plot
  • create_qq_plot
  • create_regional_plot
  • gene_set_enrichment
  • run_gwas

Delete 1 · Delete, drop, revoke or wipe things.

  • ld_pruning

Not yet classified 2 · We could not tell from the name and description.

  • annotate_snps
  • clump_snps

Files it touches

  • Any path the agent passes to its tools

Tools (44)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

  • 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_plot

    Create a Manhattan plot from GWAS summary statistics. Shows -log10(p-value) across chromosomes.

  • create_pca_plot

    Create a PCA scatter plot showing population structure. Plots PC1 vs PC2.

  • create_qq_plot

    Create a Quantile-Quantile (QQ) plot from GWAS p-values. Shows observed vs expected p-values.

  • create_regional_plot

    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.

Show 29 more tools
  • 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_gwas

    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.

Signals

Stars
1
Forks
2
Open issues
1
Weekly downloads
88
Last commit
Feb 9, 2026 (8 months ago)
Last release
Feb 9, 2026 (8 months ago)
Last package publish
Feb 9, 2026 (8 months ago)

From GitHub (fetched Oct 24, 2026) and the package registry.

Details

Registry name
io.github.zaeyasa/gwas-mcp
Version
1.0.2
Auth
No auth
Packages
pypi gwas-mcp
License
MIT
Repository
github.com/zaeyasa/gwas-mcp
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
Official MCP Registrygithub-graphql
Cite this page

GWAS Bioinformatics MCP Server. Agent Mart. https://agentmart.dev/connectors/zaeyasa-gwas-mcp (last updated 2026-10-24)