| name | gnomad-database |
| description | 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).
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gnomAD Database
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.- 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 (e.g.,
). Alternately, you may provide an .
