analyze_gwas_locus

Analyze GWAS locus variants to rank them by regulatory impact for fine-mapping and causal variant identification.

Instructions

Analyze all variants in a GWAS locus.

Ranks variants by regulatory impact for fine-mapping and causal variant identification.

Perfect for: GWAS follow-up, fine-mapping, identifying causal variants.

Example: "Analyze GWAS locus with 10 variants"

Input Schema

TableJSON Schema

Name	Required	Description	Default
`variants`	Yes
`chromosome`	No
`start`	No
`end`	No

Implementation Reference

src/index.ts:184-189 (handler)
MCP CallTool request handler case for 'analyze_gwas_locus': validates input (implicitly via schema), calls AlphaGenomeClient.analyzeGwasLocus, and returns JSON-formatted result.
```
case 'analyze_gwas_locus': {
  const result = await getClient().analyzeGwasLocus(args);
  return {
    content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
  };
}
```

src/tools.ts:334-366 (schema)

Tool schema and definition: specifies name, description, input schema with variants array (required), optional chromosome/start/end for locus.

export const ANALYZE_GWAS_LOCUS_TOOL: Tool = {
  name: 'analyze_gwas_locus',
  description: `Analyze all variants in a GWAS locus.

Ranks variants by regulatory impact for fine-mapping and causal variant identification.

Perfect for: GWAS follow-up, fine-mapping, identifying causal variants.

Example: "Analyze GWAS locus with 10 variants"`,
  inputSchema: {
    type: 'object',
    properties: {
      variants: {
        type: 'array',
        items: {
          type: 'object',
          properties: {
            chromosome: { type: 'string' },
            position: { type: 'number' },
            ref: { type: 'string' },
            alt: { type: 'string' },
          },
          required: ['chromosome', 'position', 'ref', 'alt'],
        },
        minItems: 1,
      },
      chromosome: { type: 'string' },
      start: { type: 'number' },
      end: { type: 'number' },
    },
    required: ['variants'],
  },
};

src/index.ts:99-101 (registration)
MCP ListTools request handler that registers and exposes all tools, including analyze_gwas_locus via ALL_TOOLS import.
```
server.setRequestHandler(ListToolsRequestSchema, async () => {
  return { tools: ALL_TOOLS };
});
```

src/tools.ts:709-730 (registration)

Central registration array ALL_TOOLS that includes ANALYZE_GWAS_LOCUS_TOOL for exposure via MCP ListTools.

export const ALL_TOOLS: Tool[] = [
  PREDICT_VARIANT_TOOL,
  BATCH_SCORE_TOOL,
  ASSESS_PATHOGENICITY_TOOL,
  PREDICT_TISSUE_SPECIFIC_TOOL,
  COMPARE_VARIANTS_TOOL,
  PREDICT_SPLICE_IMPACT_TOOL,
  PREDICT_EXPRESSION_IMPACT_TOOL,
  ANALYZE_GWAS_LOCUS_TOOL,
  COMPARE_ALLELES_TOOL,
  BATCH_TISSUE_COMPARISON_TOOL,
  PREDICT_TF_BINDING_IMPACT_TOOL,
  PREDICT_CHROMATIN_IMPACT_TOOL,
  COMPARE_PROTECTIVE_RISK_TOOL,
  BATCH_PATHOGENICITY_FILTER_TOOL,
  COMPARE_VARIANTS_SAME_GENE_TOOL,
  PREDICT_ALLELE_SPECIFIC_EFFECTS_TOOL,
  ANNOTATE_REGULATORY_CONTEXT_TOOL,
  BATCH_MODALITY_SCREEN_TOOL,
  GENERATE_VARIANT_REPORT_TOOL,
  EXPLAIN_VARIANT_IMPACT_TOOL,
];

src/alphagenome-client.ts:316-322 (helper)

AlphaGenomeClient helper method that bridges to Python subprocess for 'analyze_gwas_locus' action.

async analyzeGwasLocus(params: any): Promise<any> {
  try {
    return await this.callPythonBridge('analyze_gwas_locus', params);
  } catch (error) {
    if (error instanceof ApiError) throw error;
    throw new ApiError(`GWAS locus analysis failed: ${error}`, 500);
  }

AlphaGenome MCP Server