onekgpd

SUMMARY

What it does

This skill queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. It supports finding variants carried in a region (cohort-wide or within specified individuals), finding which individuals carry variants matching criteria, identifying homozygous-reference individuals at a position, and determining relatedness between two individuals. Variant results include 1000 Genomes allele frequencies, gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations. The skill requires Python >=3.11 and uses uv to run scripts. Variant and sample queries require outbound network access to a public 1000 Genomes query endpoint over TLS; sample/population metadata commands run offline using bundled data. No credentials or API keys are required. The skill is distributed under the MIT license.