onekgpd
onekgpd queries the 1000 Genomes Project cohort (3,202 whole-genome-sequenced individuals) to identify variants in a region and the individuals who carry them. Filter by allele frequency, consequence, AlphaMissense score, ClinVar significance, and zygosity; retrieve gnomAD annotations and kinship coefficients. Requires GRCh38 coordinates resolved beforehand.
onekgpd finds which 1000 Genomes individuals carry variants matching your criteria in a genomic region.
AI-generated summary based on this skill's SKILL.md
Decision gist · record as of 2026-07-28
onekgpd finds which 1000 Genomes individuals carry variants matching your criteria in a genomic region. onekgpd queries the 1000 Genomes Project cohort (3,202 whole-genome-sequenced individuals) to identify variants in a region and the individuals who carry them. Filter by allele frequency, consequence, AlphaMissense score, ClinVar significance, and zygosity; retrieve gnomAD annotations and kinship coefficients. Requires GRCh38 coordinates resolved beforehand.
Use it when
- Yes.
- onekgpd returns sample metadata including population and superpopulation information for each individual.
Verify before relying
Read SKILL.md below before installing (6 files). Open directory: indexed for reading, not audited.
Install
K-Dense-AI/scientific-agent-skills/onekgpd · repository language: Python
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Frequently asked questions
AI-generated answers based on this skill's SKILL.md and metadata
How do I query 1000 Genomes Project variants by individual?
onekgpd lets you search the 1000 Genomes cohort (3,202 whole-genome-sequenced individuals) to find which samples carry variants matching your criteria. Specify a genomic region in GRCh38 coordinates, then filter by allele frequency, consequence, AlphaMissense score, ClinVar pathogenicity, and zygosity to narrow results to the individuals you want.
Can onekgpd find individuals carrying specific variants?
Yes. onekgpd identifies which 1000 Genomes individuals carry variants in your region of interest. You can filter by gnomAD allele frequency, VEP consequence, pathogenic annotations, and whether samples are homozygous or heterozygous, then retrieve the matching sample IDs and their genotypes.
What metadata does onekgpd provide for 1000 Genomes samples?
onekgpd returns sample metadata including population and superpopulation information for each individual. You can also compute kinship coefficients and relatedness between samples to understand population structure and family relationships within the 1000 Genomes cohort.
How do I filter variants by allele frequency and pathogenicity in onekgpd?
onekgpd supports filtering by gnomAD allele frequency, ClinVar significance, AlphaMissense scores, and VEP consequence categories. Combine these filters with zygosity selection (homozygous, heterozygous, or both) to isolate variants of interest and the individuals who carry them.
What assembly and coordinates does onekgpd use?
onekgpd queries the 1000 Genomes Project using GRCh38 coordinates. You must provide genomic regions in GRCh38 format; the skill does not perform coordinate conversion, so resolve your positions beforehand if working from an older assembly.
Can onekgpd search for pathogenic variants across the 1000 Genomes cohort?
Yes. onekgpd searches the 1000 Genomes cohort for pathogenic variants by filtering on ClinVar significance, consequence type, and AlphaMissense scores. Specify your region in GRCh38 coordinates and apply these annotations to identify clinically relevant variants and count how many individuals carry them.
SKILL.md
Rendered from the published skill. Quoted content, verbatim.
OneKGPd: Individual-Level Queries over the 1000 Genomes Project
Scope
This skill queries the
(truncated - see the full file via the links below)
File tree — 6 files
skills/onekgpd/SKILL.md
skills/onekgpd/assets/kgpe.json
skills/onekgpd/references/annotation_vocabularies.md
skills/onekgpd/references/onekgpd_commands.md
skills/onekgpd/scripts/onekgpd_api.py
skills/onekgpd/scripts/onekgpd_meta.py
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