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OneKGPd — Individual-Level 1000 Genomes Queries

A Claude skill for querying the 1000 Genomes Project cohort (3,202 whole genomes, GRCh38) at the level of individual participants and variants.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Queries the extended high-coverage 1000 Genomes cohort (3,202 samples, GRCh38) at individual resolution.
  • Returns either the variants carried in a region (select-variants, select-variants-in-samples) or the individuals who carry variants matching your criteria (select-samples).
  • Filters by 1000 Genomes AF, gnomAD v4.1 exome/genome AF, VEP impact/consequence/biotype, ClinVar significance, and AlphaMissense score or class; zygosity can be restricted to het-only or hom-only.
  • Also supports homozygous-reference lookups at a single position, pairwise relatedness (degree + KING kinship coefficient), and dataset totals.
  • Population, sex, and pedigree metadata are answered offline from a bundled data file.

Who it's for

  • Human genetics and population-genomics researchers and graduate students.
  • Bioinformatics or clinical-genetics practitioners who need a fast carrier survey over a gene region.
  • Pipeline builders using 1000 Genomes as a reference cohort.

Example uses

  1. "How many individuals carry AlphaMissense likely-pathogenic missense variants in BRCA1 (chr17:43044292-43170245)?" → count-samples, then select-samples.
  2. "Which variants do HG03169 and NA20506 actually carry in that region?" → select-variants-in-samples --samples HG03169,NA20506.
  3. "Pull the YRI population sample list, then find their rare variants (AF < 0.01)" → select-samples-by-population → select-variants-in-samples --af-lt 0.01.
  4. "What is the relatedness between NA19240 and HG00096?" → kinship.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/onekgpd/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/onekgpd folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/onekgpd/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/onekgpd ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Install Python 3.11+ and uv (macOS/Linux: curl -LsSf https://astral.sh/uv/install.sh | sh).
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill into your Claude skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/onekgpd ~/.claude/skills/
  4. Confirm SKILL.md, scripts/, and references/ exist under ~/.claude/skills/onekgpd.
  5. Restart Claude Code and sanity-check connectivity with uv run scripts/onekgpd_api.py dataset-info (requires outbound network).
  6. Always resolve gene symbols to GRCh38 coordinates with an authoritative source (e.g. Ensembl) before querying — GRCh37 coordinates silently return wrong regions.
View source on GitHub ↗License: MIT