LabscoMCP early access ↗
dnaerysMCP SERVER · OFFICIAL PROJECT

OneKGPd-MCP

Ask natural-language questions of the full 1000 Genomes 30x GRCh38 call set — variants, genotypes, samples and population statistics, hosted and open.

by dnaerys ↗Biomedical: Genomics & Clinical Data✓ Official

LABSCO SUMMARY

The compute happens at the store, not in the model.

Burden scoring, AlphaMissense averaging and kinship are tools rather than something an agent assembles from raw genotype dumps — which is what makes questions spanning a whole cohort answerable at all. Two deliberate choices show the same instinct: HGVSp is restricted to canonical transcripts specifically to reduce what the model has to hold, and the population tools exist so cohort structure can be established before variants are pulled. The example prompts in the README are unusually demanding, and they are the honest indication of what this is for.

What it is

A remote MCP service over the 1000 Genomes Project dataset held in the Dnaerys variant store: 3202 samples sequenced and aligned by the New York Genome Center, 2504 unrelated from the phase three panel plus 698 from 602 family trios. Variants come annotated by VEP 115 against GENCODE 49, with ClinVar clinical significance, gnomAD frequencies and AlphaMissense scores and classes.

What you get

  • Variant and genotype selection — findVariants and findVariantsInSamples, filtered by coordinates, annotations, zygosity and population
  • Sample-side queries: findSamples, findSamplesHomozygousReference, findSamplesByPopulation, getSampleMetadata
  • Cohort computations run server-side — computeAlphaMissenseAvg and computeVariantBurden, plus getKinshipDegree for relatedness
  • Population reference data through listPopulations, listSuperpopulations, getPopulationStats and getSuperpopulationSummary
  • getDatasetInfo for what the store actually contains
  • Returned variants carry HGVSp annotations restricted to canonical transcripts, gnomAD exome and genome frequencies, AlphaMissense scores and cohort-wide statistics; samples carry family id, gender, parental ids, relationship, children, population, superpopulation and the phase three indicator

Requirements

Nothing — the hosted service is at https://db.dnaerys.org/mcp over Streamable HTTP, with no authentication and no user data collected. Running it yourself needs JRE 21 and a Maven build producing onekgpd-mcp-runner.jar as an uber-jar; the dev profile enables both stdio and HTTP transports, with HTTP on port 9000. Claude Desktop should use the stdio route against the local jar — the README notes it will not work against the local HTTP option. Apache 2.0.

Setup effort

Build from source — git clone https://github.com/dnaerys/OneKGPd-MCP.git

See installation options