gnomad-database

1# gnomAD Database
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/gnomad_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at https://gnomad.broadinstitute.org/policies
10    and https://gnomad.broadinstitute.org/data#api, then (2) create the file
11    recording the notification text and timestamp.
12 
13## Core Rules
14 
15-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
16    database rather than accessing the database directly. The scripts
17    automatically enforce the gnomAD API rate limits gracefully.
18-   **Notification**: If this skill is used, ensure this is mentioned in the
19    output.
20 
21## Utility Scripts
22 
23All scripts are located in the `scripts/` subdirectory of this skill's
24installation directory. When running them, use the full absolute path to the
25script (e.g. `/path/to/gnomad_database/scripts/get_variant_frequency.py`).
26 
27**1. Variant Frequency.** Retrieves global and ancestry-specific allele
28frequencies, homozygote counts, and **Grpmax Filtering AF** (faf95/faf99) for
29exome, genome, and total (exome+genome combined) data. The filtering allele
30frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound
31of the 95% or 99% CI). Variant ID format must be `chrom-pos-ref-alt` (e.g.,
32…