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OsmosyOsmosy/vector-gene/skills/science/gnomad_database/SKILL.md

gnomad-database

Skill0 starsChanged 25 days agoApache-2.0View on GitHub

Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).

6 other projects use a version of this, 2 of them edited.

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The file

We split this skill into the rules it gives an agent

5 rules. 0 are common, 2 are distinctive, and 3 are very specific to this project.

  • 0

    Common

    Most of the 5 edited versions we read keep these.

  • 2

    Distinctive

    This author's own choices. Worth a look.

  • 3

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Very specific:

    uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.

    line 16
  2. Very specific:

    User Notification: If .licenses/gnomad_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently …

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  3. Distinctive:

    Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly.

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  4. Distinctive:

    Notification: If this skill is used, ensure this is mentioned in the output.

    line 29
  5. Very specific:

    All scripts are located in the scripts/ subdirectory of this skill's installation directory.

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“Common” is measured: kept by at least 6 in 10 of the 5 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

gnomAD Database

Prerequisites

  1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
  2. User Notification: If .licenses/gnomad_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://gnomad.broadinstitute.org/policies and https://gnomad.broadinstitute.org/data#api, then (2) create the file recording the notification text and timestamp.

Core Rules

  • Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the gnomAD API rate limits gracefully.
  • Notification: If this skill is used, ensure this is mentioned in the output.

Utility Scripts

All scripts are located in the scripts/ subdirectory of this skill's installation directory. When running them, use the full absolute path to the script (e.g. /path/to/gnomad_database/scripts/get_variant_frequency.py).

1. Variant Frequency. Retrieves global and ancestry-specific allele frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for exome, genome, and total (exome+genome combined) data. The filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound of the 95% or 99% CI). Variant ID format must be chrom-pos-ref-alt (e.g., 1-55516888-G-GA). Alternately, you may provide an rsID.

# By variant ID:
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json

# By rsID (e.g., rs1800562):
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json

2. Gene Constraint. Retrieves constraint metrics for a gene. The response will explicitly contain pli, and the LOEUF score is represented by oe_lof_upper.

uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json

3. Region/Gene Variant Search. Finds all variants in a region or gene.

# By region:
uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json
# By gene:
uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.json

References

Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help

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