Agent skill · research science · k-dense-ai
onekgpd
Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.
Why this skill is useful
Provides specific queries and data retrieval methods for the 1000 Genomes Project dataset that the AI wouldn't reliably generate on its own.
What it needs
Requires python installed locally. About 10k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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). …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/onekgpd