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count_variants

Get variant counts matching your filters, computed server-side to size a query before downloading data. Apply genomic region, allele frequency, and missing-data criteria, or retrieve the total count.

Instructions

Count variants matching filters, computed server-side (nothing is downloaded).

Fast way to size a query before pulling data. Filter by genomic region (reference_name + optional start/end, from list_sequences), minor- allele frequency (min_maf/max_maf) and/or max_missing_data (0–1 fraction). With no filters this returns the total variant count of the set. variant_set_db_id is a BrAPI variantSetDbId (from list_variant_sets / list_content).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
endNoRegion end position, 1-based inclusive.
startNoRegion start position, 1-based inclusive.
max_mafNoMaximum minor-allele frequency (0-1).
min_mafNoMinimum minor-allele frequency (0-1).
reference_nameNoChromosome/contig name to restrict the search to (see list_sequences).
max_missing_dataNoMaximum per-variant missing-data fraction (0-1).
variant_set_db_idYesBrAPI variantSetDbId identifying the run (MODULE§project§run) -- copy the exact string from list_variant_sets / list_content, never assemble one by hand: the middle segment is a numeric project index, not the project's name, and a wrong guess fails with an opaque HTTP 500 rather than a clear error.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed1 schema field changedv1.9.1
    • changedInput schema / properties / variant_set_db_id / description
      Previous value: -"BrAPI variantSetDbId identifying the run (MODULE§project§run); from list_variant_sets / list_content."New value: +"BrAPI variantSetDbId identifying the run (MODULE§project§run) -- copy the exact string from list_variant_sets / list_content, never assemble one by hand: the middle segment is a numeric project index, not the project's name, and a wrong guess fails with an opaque HTTP 500 rather than a clear error."
  2. First observedv1.4.16

TDQS

A4.4/5.0
Behavior4/5

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

With no annotations provided, the description carries the full behavioral burden. It discloses that counting is server-side, that nothing is downloaded, and that omitting filters returns the total variant count. This gives agents an accurate model of the operation's behavior and side effects.

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?

The description is dense but well-organized, front-loading the core purpose and then grouping related filter parameters. Each sentence contributes useful information, though some parameter details overlap with the schema descriptions.

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

Completeness5/5

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

Given the presence of an output schema and a 100% schema-covered input, the description provides all the contextual information an agent needs: what the tool does, when to use it, how filters compose, and where identifier values come from. Nothing essential is missing.

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

Parameters4/5

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

Schema coverage is 100%, but the description adds meaningful context beyond the schema: it states that reference_name, start, and end come from list_sequences, that variant_set_db_id is a BrAPI variantSetDbId from list_variant_sets/list_content, and that no filters yields the total count. This helps agents correctly map parameters to domain sources.

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 uses a specific verb plus resource ('Count variants matching filters') and clearly states what makes it distinct: it is computed server-side and nothing is downloaded. This makes it easy to differentiate from siblings like search_variants or export_genotypes.

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

Usage Guidelines4/5

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

The description explicitly frames this as 'a fast way to size a query before pulling data,' which gives clear guidance on when to use it. It does not name specific sibling alternatives that should be used instead, but the use case is sufficiently clear.

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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