| --- |
| license: cc0-1.0 |
| task_categories: |
| - tabular-classification |
| tags: |
| - genomics |
| - dbsnp |
| - rsid |
| - cross-build |
| - GRCh37 |
| - GRCh38 |
| - bioinformatics |
| - sqlite |
| pretty_name: Allelix rsID Identity Table |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # Allelix rsID Identity Table |
|
|
| Pre-built SQLite cache mapping rsID allele positions between GRCh37 and GRCh38 genome builds, derived from [dbSNP build 157](https://www.ncbi.nlm.nih.gov/snp/) for use with [Allelix](https://github.com/dial481/allelix). |
|
|
| ## What's in the file |
|
|
| `rsid_identity.sqlite.gz` is a gzipped SQLite database containing the `rsid_identity` table with 4,851,120 rows covering 3,046,373 rsIDs that appear in at least one Allelix annotation database (ClinVar, GWAS Catalog, SNPedia, PharmGKB). |
|
|
| ### Schema |
|
|
| ```sql |
| CREATE TABLE rsid_identity ( |
| rsid TEXT NOT NULL, |
| chrom TEXT NOT NULL, |
| pos37 INTEGER NOT NULL, |
| ref37 TEXT NOT NULL, |
| alt37 TEXT NOT NULL, |
| pos38 INTEGER NOT NULL, |
| ref38 TEXT NOT NULL, |
| alt38 TEXT NOT NULL, |
| palindromic INTEGER NOT NULL |
| ); |
| |
| CREATE INDEX idx_rsid_identity_rsid ON rsid_identity(rsid); |
| CREATE INDEX idx_rsid_identity_pos37 ON rsid_identity(chrom, pos37); |
| CREATE INDEX idx_rsid_identity_pos38 ON rsid_identity(chrom, pos38); |
| ``` |
|
|
| ### Columns |
|
|
| | Column | Description | |
| |--------|-------------| |
| | `rsid` | dbSNP rsID (e.g. rs429358) | |
| | `chrom` | Chromosome (1-22, X, Y, MT; no "chr" prefix) | |
| | `pos37` | Genomic position on GRCh37 | |
| | `ref37` | Reference allele on GRCh37 | |
| | `alt37` | Alternate allele on GRCh37 | |
| | `pos38` | Genomic position on GRCh38 | |
| | `ref38` | Reference allele on GRCh38 | |
| | `alt38` | Alternate allele on GRCh38 | |
| | `palindromic` | 1 if the allele set equals its complement (strand-ambiguous), 0 otherwise | |
|
|
| ### Multi-allelic sites |
|
|
| An rsID with multiple alternate alleles has one row per allele. For example, rs1801133 (MTHFR C677T) has three rows for its three observed alternate alleles (A, C, T). |
|
|
| ### Inclusion criteria |
|
|
| An rsID is included only when it has exactly one primary-assembly placement per build, on the same chromosome, with allele sets that match on the same strand or (for SNVs) after complementing. Exclusions from the 3,073,779 rsID universe: |
|
|
| | Reason | Count | |
| |--------|-------| |
| | Only placed on GRCh37 | 196 | |
| | Only placed on GRCh38 | 296 | |
| | Multiple placements on one build | 685 | |
| | Alleles unpairable between builds | 205 | |
| | Chromosome changed between builds | 2 | |
|
|
| ## How Allelix uses this |
|
|
| Allelix downloads this file automatically during `allelix db update`. The identity table serves three purposes: |
|
|
| 1. **Reference allele population** for array data on both GRCh37 and GRCh38. |
| 2. **rsID recovery** for rsID-less VCF files on both builds, via locus-based lookup. |
| 3. **GRCh37 → GRCh38 coordinate translation** for cross-build enrichment against gnomAD, AlphaMissense, and CADD. Palindromic sites abstain from translation to avoid strand-ambiguous mismatches. |
|
|
| ## Building from source |
|
|
| The cache can be rebuilt from dbSNP VCFs using the build script included with Allelix: |
|
|
| ```bash |
| python scripts/build_rsid_identity_cache.py \ |
| --data-dir /path/to/dbsnp/vcfs \ |
| --output rsid_identity.sqlite \ |
| --work-dir /tmp/identity-build \ |
| --gzip |
| ``` |
|
|
| The build streams both GRCh37 and GRCh38 dbSNP VCFs through an 8 MB Bloom filter, then joins candidates in SQLite. Peak memory is ~40 MB; runtime is ~3 hours on a 1 GB VPS. |
|
|
| ## Integrity |
|
|
| | Property | Value | |
| |----------|-------| |
| | File | `rsid_identity.sqlite.gz` | |
| | Size (compressed) | 148 MB | |
| | Size (uncompressed) | 436 MB | |
| | SHA-256 | `2a00787cd0be4e7572efd21686013c49f3d0180137cd4403730524d50a5db285` | |
| | Rows | 4,851,120 | |
| | Distinct rsIDs | 3,046,373 | |
|
|
| ## Source and license |
|
|
| - **Source:** [NCBI dbSNP build 157](https://www.ncbi.nlm.nih.gov/snp/) (GRCh37 VCF: GCF_000001405.25; GRCh38 VCF: GCF_000001405.40) |
| - **License:** [CC0 1.0 / Public Domain](https://creativecommons.org/publicdomain/zero/1.0/) — derived from NCBI dbSNP, a United States Government Work in the public domain |
| - **Citation:** Sherry ST, et al. "dbSNP: the NCBI database of genetic variation." Nucleic Acids Res. 2001;29(1):308-311. |
|
|
