1000 Genomes Project Dataset MCP Server

Real time access to 1000 Genomes Project dataset, hosted online in Dnaerys variant store

Sequenced & aligned by New York Genome Center (GRCh38). 3202 samples: 2504 unrelated samples from phase three panel + 698 samples from 602 family trios (dataset details)

Key Features

real-time access to 138 044 723 unique variants and ~442 billion individual genotypes
variant, sample and genotype selection based on coordinates, annotations, zygosity
filtering by VEP (impact, biotype, feature type, variant class, consequences), ClinVar Clinical Significance (202502), gnomADe + gnomADg 4.1, AlphaMissense Score & AlphaMissense Class annotations
filtering by inheritance model (de novo, heterozygous dominant, homozygous recessive)
returned variants annotated with HGVSp, gnomADe + gnomADg, AlphaMissense score + cohort-wide statistics

Online Service

Remote MCP service via Streamable HTTP:

Architecture

Implemented as a Java EE service, accessing KGP dataset via gRPC calls to public Dnaerys variant store service.

provides MCP over Streamable HTTP, HTTP/SSE and STDIO transports
service implementation is based on Quarkus MCP Server framework

Available Tools

MCP tools and parameters are here

Installation

Project can be run locally with MCP over stdio and/or http transports

Option A - build & run locally

build the project and package it as a single über-jar:
- jar is located in target/onekgpd-mcp-runner.jar and includes all dependencies

./mvnw package -DskipTests -Dquarkus.package.jar.type=uber-jar

run it locally with dev profile
- both stdio and http transports are enabled
- http transport is on quarkus http.port
- project expects JRE 21 to be available at runtime

java -Dquarkus.profile=dev -jar <full path>/onekgpd-mcp-runner.jar

Option B - build & run in docker

in order to run in docker, stdio transport needs to be disabled to prevent application from stopping itself due to closed stdio in containers
- it's already configured in prod profile
- it's the default configuration overall
build with prod profile

docker build -f Dockerfile -t onekgpd-mcp .

run as you prefer, e.g.

docker run -p 9000:9000 --name onekgpd-mcp --rm onekgpd-mcp

Option C - pull from Docker Hub

pull prebuilt image; stdio transport disabled, http transport on port 9000

docker pull dnaerys/onekgpd-mcp:latest

docker run -p 9000:9000 --name onekgpd-mcp --rm onekgpd-mcp

Connecting with MCP clients

to connect via http transport, remote or local, simply direct the client to a destination, e.g. http://localhost:9000/mcp or https://db.dnaerys.org:443/mcp
to connect via stdio transport, MCP client should start application with dev profile and with a full path to the jar file
- e.g. add to Claude config files (e.g. claude_desktop_config.json):

{
  "mcpServers": {
    "OneKGPd": {
      "command": "java",
      "args": ["-Dquarkus.profile=dev", "-jar", "/full/path/onekgpd-mcp-runner.jar"]
    }
  }
}

Verification

How many variants exist in 1000 Genome Project ?

License

This project is licensed under the Apache License 2.0 - see the LICENSE file for details.

OneKGP