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AlphaGenome MCP Server

by taehojo
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TypeScript
Remote

batch_score_variants

Score up to 100 genomic variants and rank them by predicted effect, returning separate rankings for Atlas and live inference sources with counts for each.

Instructions

Score up to 100 variants and rank them by predicted effect.

Each variant is routed on its own: single-nucleotide variants to the Atlas, the rest to live inference. A mixed batch comes back as two separately ranked groups, because the Atlas group is ranked by the AVI score and live inference has no AVI score; the two must not be compared. The result reports how many variants came from each source and how many fell back.

Scoring metric (used when scorers is not given): rna_seq = RNA_SEQ, splice = SPLICE_SITES, regulatory_impact and combined = AVI_SCORE from the Atlas and every modality (ranked by the largest absolute quantile) from live inference.

Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made.

Example: "Score these 50 variants and show me the top 10 by predicted effect"

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
top_nNoVariants to return per group (default: 10, max: 100)
sourceNoOptional: where the answer comes from (default: auto). auto = the precomputed AlphaGenome Atlas for single-nucleotide substitutions, live inference for everything else (indels, multi-nucleotide variants); falls back to live only when the Atlas does not hold the variant. atlas = Atlas only, errors instead of falling back. live = always run the model. The result always states which source answered.
scorersNoOptional: scorer names to use instead of the defaults. Names come from atlas_list_scorers and are the same for both sources, except the AVI scorers, which the Atlas alone serves.
variantsYesVariants to score (1-100)
scoring_metricYesWhat to rank by

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed10 schema fields changedv0.3.0
    • removedInput schema / properties / include_interpretation
      Removed value: -{
-  "description": "Include detailed clinical interpretation (default: false)",
-  "type": "boolean"
-}
    • addedInput schema / properties / scorers
      Added value: +{
+  "description": "Optional: scorer names to use instead of the defaults. Names come from atlas_list_scorers and are the same for both sources, except the AVI scorers, which the Atlas alone serves.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}
    • changedInput schema / properties / scoring_metric / description
      Previous value: -"Metric to use for scoring and ranking"New value: +"What to rank by"
    • addedInput schema / properties / source
      Added value: +{
+  "description": "Optional: where the answer comes from (default: auto). auto = the precomputed AlphaGenome Atlas for single-nucleotide substitutions, live inference for everything else (indels, multi-nucleotide variants); falls back to live only when the Atlas does not hold the variant. atlas = Atlas only, errors instead of falling back. live = always run the model. The result always states which source answered.",
+  "enum": [
+    "auto",
+    "atlas",
+    "live"
+  ],
+  "type": "string"
+}
    • changedInput schema / properties / top_n / description
      Previous value: -"Number of top variants to return (default: 10, max: 100)"New value: +"Variants to return per group (default: 10, max: 100)"
    • changedInput schema / properties / variants / description
      Previous value: -"List of variants to analyze (1-100)"New value: +"Variants to score (1-100)"
    • changedInput schema / properties / variants / items / properties / alt / description
      Previous value: -"Alternate allele"New value: +"Alternate allele (A, C, G, T; more than one base for an indel)"
    • changedInput schema / properties / variants / items / properties / chromosome / description
      Previous value: -"Chromosome"New value: +"Chromosome (chr1-chr22, chrX, chrY)"
    • changedInput schema / properties / variants / items / properties / position / description
      Previous value: -"Position"New value: +"Genomic position (1-based, hg38)"
    • changedInput schema / properties / variants / items / properties / ref / description
      Previous value: -"Reference allele"New value: +"Reference allele (A, C, G, T; more than one base for an indel)"
  2. First observed

TDQS

A3.9/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It discloses key non-obvious behaviors: per-variant routing, two non-comparable ranked groups (AVI vs live), fallback counts in the result, and that outputs are predictions not clinical classifications. It does not cover rate limits, permissions, or error behavior for atlas-only mode.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with purpose followed by routing rules, metric mapping, and a disclaimer. Four paragraphs are justified by the genuinely complex behavior, though the example at the end is somewhat redundant given the clear opening sentence.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a 5-param tool with no output schema and no annotations, the description covers routing, grouping semantics, metric defaults, and the research-use limitation. Missing pieces are minor: no explanation of output fields beyond source counts, and no explicit prerequisite guidance.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents each parameter, and the description's metric mapping (rna_seq → RNA_SEQ, etc.) largely restates the enum. The description adds marginal value by clarifying that scorers come from atlas_list_scorers and that AVI scorers are Atlas-only, but this is mostly schema-adjacent rather than new semantics.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb+resource+scope: 'Score up to 100 variants and rank them by predicted effect.' The batch nature and the 100-variant cap distinguish it from single-variant siblings, and the routing detail (Atlas vs live inference) further differentiates it.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explains internal routing behavior and the two-group result, but does not state when to use this over sibling batch tools like batch_pathogenicity_filter or batch_modality_screen, nor when a user should prefer single-variant predict_variant_effect. Usage is implied by the batch scope rather than explicitly guided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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