onekgpd

OneKGPd: Individual-Level Genome Query Tool for the 1000 Genomes Project

Skill Overview

OneKGPd is a specialized skill tool for querying datasets from the 1000 Genomes Project. It supports individual-level variant data queries for 3,202 whole-genome sequenced individuals (GRCh38 build).

Use Cases

Disease-Related Variant Research

Query individuals carrying potentially pathogenic variants in specific genes or regions. Supports filtering by AlphaMissense score, ClinVar clinical significance, and allele frequency.

Population Genetics Analysis

Analyze variant distributions across different populations and super-populations; query variant carriers in specific populations. Supports sample filtering from 26 populations and 5 super-populations.

Individual Genetics Research

Query genome variants of a specific individual, analyze genetic relatedness between individuals, and identify individuals with homozygous reference genotypes.

Core Capabilities

Variant Query and Filtering

Supports querying variants by region. Enables multi-dimensional filtering by allele frequency (1000 Genomes AF, gnomAD exomes/genomes AF), variant consequence, VEP annotation, clinical significance, etc., and supports filtering by heterozygous/homozygous status.

Individual Sample Query

Can query a list of individuals carrying specific variants. Supports filtering by gene region, variant type, predicted impact, and other conditions, returning individual names and related variant information.

Relatedness and Metadata Analysis

Supports relatedness analysis between two individuals (identical twins, first-degree, second-degree, third-degree relatives, and unrelated individuals) and calculation of KING relatedness coefficients. Provides metadata queries such as population, sex, and family pedigree (no network connection required).

Frequently Asked Questions

What types of genome queries does OneKGPd support?

OneKGPd supports querying individuals carrying specific variants, querying variants carried by specific individuals, calculating the number of variants and individuals, analyzing relatedness between individuals, and querying population and sex metadata. Queries can be filtered across multiple dimensions, including allele frequency, variant consequence, clinical significance, and AlphaMissense classification.

How do I query gene variant data using GRCh38 coordinates?

Before using OneKGPd, you must first map gene symbols or transcripts to GRCh38 coordinates from authoritative sources (such as Ensembl). Then use the --chrom, --start, and --end parameters to specify a region, optionally adding variant filtering criteria. It is recommended to first run a counting command (e.g., count-variants) to estimate the result set size, and then run the selection command (e.g., select-variants).

Does OneKGPd require an API key or authentication?

No. OneKGPd performs network queries using the public 1000 Genomes query endpoints, while sample and population metadata queries are fully offline (using embedded data files within the skill package). No API key, environment variables, or authentication configuration are required—only installing Python >=3.11 and the uv tool.