@cyanheads/gnomad-genetics-mcp-server
by cyanheads
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_API_KEY | No | Optional NCBI key. Raises the E-utilities rate limit from 3 to 10 req/s. | |
| OTEL_ENABLED | No | Enable OpenTelemetry instrumentation. | false |
| MCP_AUTH_MODE | No | Auth mode: none, jwt, or oauth. | none |
| MCP_HTTP_PORT | No | Port for the HTTP server. | 3010 |
| MCP_LOG_LEVEL | No | Log level (RFC 5424). | info |
| CLINVAR_BASE_URL | No | NCBI E-utilities base URL for gnomad_search_clinvar. | https://eutils.ncbi.nlm.nih.gov/entrez/eutils |
| MCP_TRANSPORT_TYPE | No | Transport: stdio or http. | stdio |
| GNOMAD_API_BASE_URL | No | gnomAD GraphQL endpoint. Override for a private mirror or testing. | https://gnomad.broadinstitute.org/api |
| CANVAS_PROVIDER_TYPE | No | Set to duckdb to enable the spill/SQL path behind the list tools. When none, they return a capped inline preview. | none |
| GNOMAD_DEFAULT_DATASET | No | Dataset used when a tool call omits dataset (gnomad_r4 / gnomad_r3 / gnomad_r2_1 / exac). | gnomad_r4 |
| GNOMAD_MAX_CONCURRENCY | No | Cap on concurrent upstream requests — politeness against a community-funded API. | 2 |
| GNOMAD_MAX_VARIANT_BATCH | No | Maximum variant IDs accepted per gnomad_get_variant call. | 25 |
| GNOMAD_REQUEST_TIMEOUT_MS | No | Per-request timeout against the GraphQL endpoint, in milliseconds. | 30000 |
| GNOMAD_DATAFRAME_DROP_ENABLED | No | Gate for the opt-in gnomad_dataframe_drop tool. Off by default. | false |
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
No tools | |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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