Update README.md

README.md

@@ -1,3 +1,91 @@
 ---
 license: odbl
+task_categories:
+  - tabular-classification
+tags:
+  - genomics
+  - gnomad
+  - allele-frequency
+  - population-genetics
+  - bioinformatics
+  - sqlite
+pretty_name: Allelix gnomAD Exome Frequencies
+size_categories:
+  - 10M<n<100M
 ---
+
+# Allelix gnomAD Exome Frequency Cache
+
+Pre-built SQLite cache of population allele frequencies from [gnomAD v4.1 exomes](https://gnomad.broadinstitute.org/) for use with [Allelix](https://github.com/dial481/allelix).
+
+## What's in the file
+
+`exome_frequencies.sqlite.gz` is a gzipped SQLite database containing the `gnomad_frequencies` table with all ~16M exome variants that carry an rsID in gnomAD v4.1.
+
+### Schema
+
+```sql
+CREATE TABLE gnomad_frequencies (
+    chrom TEXT NOT NULL,
+    pos INTEGER NOT NULL,
+    ref TEXT NOT NULL,
+    alt TEXT NOT NULL,
+    rsid TEXT,
+    af REAL,
+    af_popmax REAL,
+    popmax TEXT,
+    af_afr REAL,
+    af_amr REAL,
+    af_asj REAL,
+    af_eas REAL,
+    af_fin REAL,
+    af_nfe REAL,
+    af_sas REAL,
+    PRIMARY KEY (chrom, pos, ref, alt)
+);
+
+CREATE INDEX idx_gnomad_rsid ON gnomad_frequencies(rsid);
+```
+
+### Columns
+
+| Column | Description |
+|--------|-------------|
+| `chrom` | Chromosome (1-22, X, Y, no "chr" prefix) |
+| `pos` | Genomic position (GRCh38) |
+| `ref` | Reference allele |
+| `alt` | Alternate allele |
+| `rsid` | dbSNP rsID |
+| `af` | Global allele frequency |
+| `af_popmax` | Maximum allele frequency across populations |
+| `popmax` | Population with the highest frequency |
+| `af_afr` | African/African American frequency |
+| `af_amr` | Admixed American/Latino frequency |
+| `af_asj` | Ashkenazi Jewish frequency |
+| `af_eas` | East Asian frequency |
+| `af_fin` | Finnish frequency |
+| `af_nfe` | Non-Finnish European frequency |
+| `af_sas` | South Asian frequency |
+
+### Multi-allelic sites
+
+The composite primary key `(chrom, pos, ref, alt)` preserves multi-allelic sites. A single rsID may have multiple rows with different alternate alleles. For example, rs776646858 has 13 distinct ALT alleles in the exome dataset.
+
+## How Allelix uses this
+
+Allelix downloads this file automatically during `allelix db update`. The annotator looks up variants by rsID and returns `MAX(af)` across alleles for a given rsID. Coordinate columns are indexed for future integration with AlphaMissense and CADD scores.
+
+## Building from source
+
+The cache can be rebuilt from gnomAD exome VCFs using the build script included with Allelix:
+
+```bash
+python scripts/build_gnomad_cache.py --full --local-dir /path/to/gnomad/vcfs --output exome_frequencies.sqlite
+gzip exome_frequencies.sqlite
+```
+
+## Source and license
+
+- **Source:** [gnomAD v4.1 exomes](https://gnomad.broadinstitute.org/) (Broad Institute)
+- **License:** [Open Data Commons Open Database License (ODbL) v1.0](https://opendatacommons.org/licenses/odbl/1-0/)
+- **Citation:** See [gnomAD papers](https://gnomad.broadinstitute.org/publications)