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onekgpd
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Queries 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.
When to use
- 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 (fo…
- Find **variants** carried in a region or set of regions matching some criteria
- Find **which 1000 Genomes individuals** carry variants matching some criteria
- Count how many individuals carry specific variants (`count-samples`).
- Restrict any variant query to **heterozygous-only or homozygous-only**
- Identify which individuals are **homozygous reference** at a single position
- Determine the **relatedness** between two named 1000 Genomes individuals —
- Get **dataset totals** — sample count, sex split, variant count, assembly
When not to use
- Resolving gene symbols or rsIDs to coordinates
- Fetching reference sequence
- Querying cohorts other than the 1000 Genomes Project
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