| --- |
| license: other |
| license_name: ensembl-unrestricted-and-loftee-mit |
| license_details: Ensembl data are freely available without restriction; LOFTEE resources are from an MIT-licensed project. See the Licensing section below. |
| language: |
| - en |
| tags: |
| - genomics |
| - ensembl |
| - vep |
| - loftee |
| - GRCh38 |
| - reference-data |
| pretty_name: VEP 113 GRCh38 reference bundle (cache, FASTA, LOFTEE) |
| --- |
| |
| # VEP 113 / GRCh38 reference bundle — cache, FASTA, LOFTEE data |
|
|
| A fast mirror of the reference data needed to run Ensembl VEP release 113 |
| offline on GRCh38, in the prepared forms a local annotation pipeline needs — |
| assembled for the **WES/WGS diagnostic analysis pipeline** (IEI variant-review |
| workbench), whose downloader verifies every file against pinned SHA-256 |
| checksums and falls back to the canonical sources automatically. |
|
|
| Mirror rationale: the canonical servers often serve well under 1 MiB/s per |
| connection transatlantically; this mirror typically saves hours on first-time |
| setup. Contents are unmodified from their sources except where noted. |
|
|
| ## Files |
|
|
| | File | Contents | Source | |
| |---|---|---| |
| | `homo_sapiens_vep_113_GRCh38.cache.tar.gz` | Ensembl VEP indexed cache, release 113, GRCh38 (retarred from the extracted official cache) | Ensembl | |
| | `Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz` (+ `.fai`, `.gzi`) | GRCh38 primary-assembly FASTA, **re-compressed as BGZF** with indexes (VEP/LOFTEE require BGZF; Ensembl ships plain gzip) | Ensembl | |
| | `human_ancestor.fa.gz` (+ `.fai`, `.gzi`) | LOFTEE GRCh38 ancestral sequence | LOFTEE (Broad) | |
| | `loftee.sql` | LOFTEE GRCh38 conservation database | LOFTEE (Broad) | |
| | `gerp_conservation_scores.homo_sapiens.GRCh38.bw` | GERP conservation bigWig for LOFTEE GRCh38 | Ensembl/LOFTEE | |
|
|
| ## Licensing and attribution |
|
|
| - **Ensembl data** (VEP cache, FASTA, GERP bigWig): Ensembl data are freely |
| available without restriction; see https://www.ensembl.org/info/about/legal/disclaimer.html. |
| Cite: McLaren et al., *The Ensembl Variant Effect Predictor*, Genome |
| Biology 17, 122 (2016), and the current Ensembl release paper. |
| - **LOFTEE data** (ancestral FASTA, conservation SQL): from the public LOFTEE |
| resources (MIT-licensed project); cite Karczewski et al., Nature 581, |
| 434–443 (2020). https://github.com/konradjk/loftee |
| - This compilation adds no restrictions. |
|
|
| ## Use with the pipeline |
|
|
| `scripts/download_references.sh` uses this mirror automatically when |
| configured, verifying each file against the SHA-256 checksums pinned in the |
| script and falling back to the canonical Ensembl/Broad sources if the mirror |
| is unavailable or fails verification. Manual use: download, verify, then |
| place the files under your configured reference locations (`vep_cache/` for |
| the extracted tarball, `fasta/`, `loftee/`). |
|
|
