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OneKGPd 1000 Genomes Queries

Query 1000 Genomes individuals and variants by gene, region, frequency and consequence

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
5 files

What it does

Once installed, the agent can answer questions about specific people and variants in the 1000 Genomes Project, a public collection of genomes from 3,202 individuals (GRCh38). It can list variants carried in a region, find which individuals carry matching variants, count them, check whether two named individuals are related, and look up population and pedigree details from a bundled file. Variant results come with allele frequencies, gnomAD values, AlphaMissense scores and HGVSp annotations.

Great for

  • Bioinformatics researchers exploring carriers of variants in a gene or region of the 1000 Genomes cohort
  • Students learning how population genetic datasets are queried
  • Analysts checking relatedness between two named 1000 Genomes samples

Skip it if

  • Converting gene symbols, rsIDs or transcripts to coordinates or fetching reference sequence, because the skill says to resolve those elsewhere first (the skill does not do this itself)
  • Clinical or diagnostic decisions about a real person, since this is research data and results are not clinically validated
  • Datasets other than the 1000 Genomes Project, which the skill does not serve

Try asking

  • “Count how many 1000 Genomes individuals carry missense variants in BRCA1 classified as likely pathogenic by AlphaMissense”
  • “Which individuals are homozygous reference at a given position on chr17?”
  • “Are samples NA19238 and NA19240 related, and what is their KING kinship coefficient?”
  • “List the superpopulations in the 1000 Genomes dataset and show sample metadata for HG00096”
Step-by-step guide: how to use OneKGPd 1000 Genomes QueriesInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 5 original files, the MIT licence and an attribution note.

    onekgpd.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip onekgpd.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip onekgpd.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Always run the count command first to size a query before selecting variants, since large selections can be slow or truncated.
  • Check for result_incomplete=true or truncated=true in the output before drawing any conclusion of absence.
  • Resolve gene coordinates from an authoritative GRCh38 source first and record the annotation releases (VEP 115, ClinVar 202502, gnomAD 4.1) when reporting results.

What's inside

  • references/annotation_vocabularies.md
  • references/onekgpd_commands.md
  • scripts/onekgpd_api.py
  • scripts/onekgpd_meta.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.