gnomad-database

Files (4)

• SKILL.md
• get_gene_constraint.py · scripts/
• get_variant_frequency.py · scripts/
• search_variants.py · scripts/

SKILL.md (first lines)

# 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 LICENSE_NOTIFICATION.txt does not already exist in
    this skill 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`.

```bash
# 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`.

```bash
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.

```bash
# 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

From hanyanphysics/AI-for-Physics, Apache-2.0.

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