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/).