// SCAN REPORT

Gwas

44 tools. 9 can modify or destroy data without limits.

9 write tools that can modify data. Rate limits recommended.

Last updated: 30 Jun 2026

9 can modify or destroy data

35 read-only

44 tools total

Community server · catalogue entry verified 30/06/2026

How to control Gwas ↓

TOOL MAP

What Gwas exposes to your agents

Read (35) Write / Execute (9) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

High Risk

The most dangerous Gwas tools

Execute · High run_gwas This tool executes non-trivial statistical computations (GWAS analysis via regression) whose effects are contingent on arguments provided by an AI agent. Execute · Medium ld_pruning The tool performs a computational operation (LD pruning) that filters/removes variants from a dataset to produce a reduced independent set. Execute · Medium calculate_heritability_ldsc This tool executes a statistical analysis algorithm (LDSC regression) on provided datasets to produce heritability estimates. Execute · Medium calculate_pca PCA for population stratification involves running an external computation engine (PLINK) on input files to produce statistical outputs.

9 of Gwas's 44 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control Gwas

PolicyLayer is an MCP gateway — it sits between your AI agents and Gwas, and nothing reaches the server without passing your rules. These are the rules we recommend:

Rate limit write operations

{
  "create_manhattan_plot": {
    "limits": [
      {
        "counter": "create_manhattan_plot_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "annotate_snps": {
    "limits": [
      {
        "counter": "annotate_snps_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register Gwas — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON GWAS →

Instant setup, no code required.

FULL CATALOGUE

All 44 Gwas tools

EXECUTE 5 tools

Execute calculate_heritability_ldsc Estimate SNP-heritability using LD Score regression. Requires GWAS summary statistics and LD scores. Execute calculate_pca Perform Principal Component Analysis for population stratification. Uses PLINK files as input. Execute clump_snps Perform LD-based clumping of GWAS results to identify independent significant signals. Execute ld_pruning Prune SNPs based on linkage disequilibrium (LD). Removes variants in high LD to create an independent set. Execute run_gwas Perform genome-wide association study using linear or logistic regression. Returns summary statistics includin

WRITE 4 tools

Write create_manhattan_plot Create a Manhattan plot from GWAS summary statistics. Shows -log10(p-value) across chromosomes. Write create_qq_plot Create a Quantile-Quantile (QQ) plot from GWAS p-values. Shows observed vs expected p-values. Write create_regional_plot Create a regional association plot (LocusZoom-style) for a specific genomic region around a lead SNP. Write gene_set_enrichment Perform gene set enrichment analysis using GO and KEGG pathways via Enrichr.

READ 35 tools

Read annotate_snps Annotate SNPs with gene names, functional consequences, and allele frequencies from Ensembl VEP and gnomAD. Read calculate_genomic_inflation Calculate genomic inflation factor (lambda GC) from GWAS summary statistics. Used to assess population stratif Read calculate_missingness Calculate per-individual and per-variant missingness rates from genotype data. Read calculate_prs Calculate Polygenic Risk Scores (PRS) for individuals using GWAS summary statistics and target genotypes. Read create_pca_plot Create a PCA scatter plot showing population structure. Plots PC1 vs PC2. Read extract_locus Extract genotype data for a specific genomic region around a lead SNP for fine-mapping. Read get_alphafold_structure Get AlphaFold AI-predicted protein structure by UniProt ID. Returns structure confidence and download links. Read get_clinvar_variant Get detailed ClinVar information for a specific variant by rsID or ClinVar ID. Read get_disease_associations Get disease associations for a gene from Open Targets with evidence scores. Read get_drug_gene_interactions Get drug-gene interaction annotations from PharmGKB for a specific gene. Read get_drug_targets Get drug target information from Open Targets for a gene. Shows drugs in development and approved drugs target Read get_eqtl_data Get expression quantitative trait loci (eQTL) data from GTEx for a SNP and tissue. Read get_functional_enrichment Get functional enrichment analysis for a list of proteins using STRING. Returns enriched GO terms, pathways, a Read get_gene_diseases Get genetic diseases associated with a gene from OMIM and other sources. Read get_gene_pathways Find all KEGG pathways that a gene participates in. Read get_interaction_network Get interaction network between a list of proteins from STRING. Shows how multiple proteins interact with each Read get_interpro_domains Get protein domain information from InterPro for a given UniProt ID or protein sequence. Read get_kegg_pathway Get detailed KEGG pathway information including genes and description. Read get_pdb_structure Get detailed information about a PDB structure by PDB ID. Read get_protein_details Get detailed protein information from UniProt by UniProt accession ID. Returns full protein details including Read get_protein_interactions Get protein-protein interaction network from STRING database. Shows what proteins interact with your protein o Read get_variant_info Get detailed variant/SNP information from Ensembl by rsID. Returns position, alleles, clinical significance, a Read identify_significant_snps Filter GWAS results to identify genome-wide significant SNPs based on p-value threshold. Read query_gwas_catalog Query the NHGRI-EBI GWAS Catalog for previously reported associations for a SNP or trait. Read search_alphafold Search AlphaFold database for predicted structures by gene name or protein name. Read search_clinvar Search ClinVar for clinical variant interpretations. Find pathogenic/benign classifications for genetic varian Read search_ensembl_gene Search Ensembl for gene information by gene symbol or Ensembl ID. Returns gene location, biotype, and descript Read search_kegg_pathway Search KEGG for metabolic and signaling pathways by name or gene. Read search_ncbi_gene Search NCBI Gene database for gene information by gene symbol, name, or ID. Read search_omim Search OMIM (Online Mendelian Inheritance in Man) for genetic diseases and phenotypes. Read search_open_targets Search Open Targets Platform for genes, diseases, or drugs. Read search_pdb_structures Search PDB for protein 3D structures by protein name, gene name, or UniProt ID. Read search_pharmgkb Search PharmGKB for drug-gene interactions and pharmacogenomics data. Read search_uniprot Search UniProt for protein information by protein name, gene name, or UniProt ID. Returns protein function, se Read vcf_quality_check Perform quality control on a VCF file. Filters variants based on MAF, missingness, and Hardy-Weinberg equilibr

EXPLORE

Related servers

Other MCP servers with similar tools — same risk classification, starter policies for each.

FAQ

Questions about Gwas

How do I prevent bulk modifications through Gwas? +

The Gwas server has 4 write tools including create_manhattan_plot, create_qq_plot, create_regional_plot. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach Gwas.

How many tools does the Gwas MCP server expose? +

44 tools across 3 categories: Execute, Read, Write. 35 are read-only. 9 can modify, create, or delete data.

How do I enforce a policy on Gwas? +

Register the Gwas MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every Gwas tool call.

Deterministic rules across all 44 Gwas tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON GWAS →

Instant setup, no code required.

44 Gwas tools catalogued and risk-classified — across an index of 43,000+ MCP servers.