generate_variant_report
Generate comprehensive clinical reports for genomic variants with full analysis, modalities, and clinical interpretation to support diagnostic summaries.
Instructions
Generate comprehensive clinical report for a variant.
Full analysis with all modalities and clinical interpretation.
Perfect for: clinical reports, diagnostic summaries.
Example: "Generate full report for chr13:32912345G>T"
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chromosome | Yes | ||
| position | Yes | ||
| ref | Yes | ||
| alt | Yes | ||
| tissue_type | No |
Implementation Reference
- src/tools.ts:662-682 (schema)Tool schema definition with input validation for chromosome, position, ref, alt, and optional tissue_type.
export const GENERATE_VARIANT_REPORT_TOOL: Tool = { name: 'generate_variant_report', description: `Generate comprehensive clinical report for a variant. Full analysis with all modalities and clinical interpretation. Perfect for: clinical reports, diagnostic summaries. Example: "Generate full report for chr13:32912345G>T"`, inputSchema: { type: 'object', properties: { chromosome: { type: 'string', pattern: '^chr([1-9]|1[0-9]|2[0-2]|X|Y)$' }, position: { type: 'number', minimum: 1 }, ref: { type: 'string', pattern: '^[ATGCatgc]+$' }, alt: { type: 'string', pattern: '^[ATGCatgc]+$' }, tissue_type: { type: 'string' }, }, required: ['chromosome', 'position', 'ref', 'alt'], }, }; - src/tools.ts:709-730 (registration)Registration of all tools including GENERATE_VARIANT_REPORT_TOOL in the ALL_TOOLS array returned by ListTools endpoint.
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/index.ts:265-271 (handler)MCP CallToolRequestSchema handler case that validates input and calls AlphaGenomeClient.generateVariantReport.
case 'generate_variant_report': { const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams; const result = await getClient().generateVariantReport(params); return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }], }; } - src/alphagenome-client.ts:448-455 (handler)AlphaGenomeClient method that proxies the tool call to Python bridge with action 'generate_variant_report'.
async generateVariantReport(params: VariantPredictionParams): Promise<any> { try { return await this.callPythonBridge('generate_variant_report', params); } catch (error) { if (error instanceof ApiError) throw error; throw new ApiError(`Variant report generation failed: ${error}`, 500); } } - scripts/alphagenome_bridge.py:658-676 (handler)Core implementation: generates variant report using assess_pathogenicity results, formats clinical classification, scores, evidence summary, and recommendations.
def generate_variant_report(client, params: Dict[str, Any]) -> Dict[str, Any]: """Generate clinical report for variant.""" result = assess_pathogenicity(client, params) # Build clinical report report = { 'variant': result['variant'], 'classification': result['classification'].upper(), 'pathogenicity_score': result['pathogenicity_score'], 'evidence_summary': { 'expression_impact': f"{result['evidence']['expression_impact']:.4f}", 'splicing_impact': f"{result['evidence']['splice_impact']:.4f}", 'tf_binding_impact': f"{result['evidence']['tf_binding_impact']:.2f}" }, 'recommendation': 'Further clinical evaluation recommended' if result['pathogenicity_score'] > 0.5 else 'Routine monitoring', 'generated_date': 'API call timestamp' } return report