onekgpd

onekgpd is a skill for Claude Code from agentlas-ai/agentlas-desktop. It costs 143 tokens per session (4,825 once invoked), scanned A, a copy of onekgpd, Apache-2.0.

A query tool for individual-level data from the 1000 Genomes Project, a large collection of whole-genome sequences from people around the world. It works with the GRCh38 human genome reference.

In plain words
What is it for?
Use it to find variants by gene or region, filter by frequency or predicted effect, select people carrying specified variants, distinguish heterozygous from homozygous calls, and check relationships.
Why use it?
It lets you ask which participants carry variants meeting particular conditions without manually inspecting genotype files. It can also compare relatedness between named participants.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

Good fit Use it to find variants by gene or region, filter by frequency or predicted effect, select people carrying specified variants, distinguish heterozygous from homozygous calls, and check relationships.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/agentlas-ai/agentlas-desktop/onekgpd
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add agentlas-ai/agentlas-desktop --skill onekgpd
Clone the repo
git clone --depth 1 https://github.com/agentlas-ai/agentlas-desktop

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for onekgpd

README.md
[![agentmods](https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/onekgpd/github.svg)](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/onekgpd)
Your own site
<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/onekgpd"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/onekgpd/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for onekgpd

Your own site · 80×15
<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/onekgpd"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/onekgpd.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 143 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,825 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 100% copy Near-identical to another mod in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00143 $0.04825
Opus 5.5 $0.00057 $0.01930
Sonnet 5.5 $0.00029 $0.00965
Haiku 4.5 $0.00014 $0.00483

Measured 1mo ago against content hash 918797c80e98, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

onekgpd scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/onekgpd_api.py, scripts/onekgpd_meta.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

100% identical to onekgpd — 109 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

plugins/agentlas-science-skills/skills/onekgpd/SKILL.md · 371 lines

How it starts

The opening of the file, as written. The whole thing — 371 lines — stays where its author put it; the contents beside it link to each section on GitHub.

OneKGPd: Individual-Level Queries over the 1000 Genomes Project

Scope

This skill queries the 1000 Genomes Project dataset — the extended high-coverage cohort of 3,202 whole-genome-sequenced individuals, on the GRCh38 assembly. All results are drawn from this cohort, and sample names returned by the skill (for example HG00096 or NA21130) identify its participants.

Queries resolve against the cohort's per-individual genotype data. This supports two complementary classes of question: selecting variants carried within a region (across the whole cohort or within a specified set of individuals), and selecting the individuals who carry variants matching given criteria. Variant selection can be filtered by allele frequency, predicted consequence, clinical significance, AlphaMissense classification, and the other annotation axes listed below. Relatedness between two named individuals is also available.

The genotype state in which a variant is carried — heterozygous or homozygous — is a criterion that queries may specify; results are returned as variants or as sample names, not as raw genotypes.

When to Use

Use this skill when you need to:

  • Find variants carried in a region or set of regions matching some criteria across the whole cohort (select-variants).
  • Find variants carried in a region or set of regions matching some criteria in specific set of individuals (select-variants-in-samples).
  • Find which 1000 Genomes individuals carry variants matching some criteria in a region or set of regions (select-samples).
  • Count how many individuals carry specific variants (count-samples).
  • Restrict any variant query to heterozygous-only or homozygous-only carriage, or query both together (default).
  • Identify which individuals are homozygous reference at a single position (select-samples-hom-ref).
  • Determine the relatedness between two named 1000 Genomes individuals — both the degree (twin / 1st / 2nd / 3rd / unrelated) and the KING kinship coefficient (kinship).
  • Get dataset totals — sample count, sex split, variant count, assembly (dataset-info).
  • Variant selection can be specified by KGP allele frequency, gnomAD 4.1 exome and gnomAD 4.1 genome allele frequency, AlphaMissense Score and AlphaMissense Class, ClinVar significance (202502), and VEP annotations (impact, biotype, feature type, variant class, consequences).

Read the full file on GitHub · 371 lines

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago First seen · 371 lines · 143 tokens per session scan A 918797c80e98

Subscribe to this mod's changes

onekgpd is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 143 tokens to every session and 4,825 once invoked, about $0.0006 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to onekgpd, differing in 109 lines, and is treated as a copy.

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