onekgpd
Category: scientific-databases · License: MIT · Version: 1.2 · Includes scripts
Tags: 1000 Genomes, population genetics, genomic variants, human genomics
When to use it
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.Example requests
Ask your agent in plain language, for example:- “Who in 1000 Genomes is homozygous for rare missense variants in CFTR? Rare = gnomAD genome AF under 0.1%.”
- “kinship HG00096 NA21130”
- “I’m following up a hit in BRCA1 for a paper. I have the region chr17:43044295-43125364 from an old UCSC hg19 browser session. I want to see which variants ClinVar calls pathogenic or likely pathogenic that are carried by HG00096, HG00097 and NA12878 in the 1000 Genomes high-coverage cohort, with their AlphaMissense scores.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole scientific-databases category with /plugin install scientific-databases@research-agent-skills.