| --- |
| license: other |
| pretty_name: Ensembl variation (split parquet) |
| tags: |
| - genomics |
| - variants |
| - GRCh38 |
| configs: |
| - config_name: core |
| data_files: data/*.parquet |
| default: true |
| - config_name: consequence |
| data_files: groups/consequence/*.parquet |
| - config_name: clinical |
| data_files: groups/clinical/*.parquet |
| - config_name: predictors |
| data_files: groups/predictors/*.parquet |
| - config_name: cadd |
| data_files: groups/cadd/*.parquet |
| - config_name: frequency |
| data_files: groups/frequency/*.parquet |
| - config_name: frequency_populations |
| data_files: groups/frequency_populations/*.parquet |
| - config_name: transcripts |
| data_files: groups/transcripts/*.parquet |
| --- |
| |
| # Ensembl variation, split parquet |
|
|
| dbSNP variants for GRCh38 with Ensembl VEP annotations, converted from the Ensembl variation VCF |
| (`variation.vcf.gz`, release directory `2026_07_13`) into |
| parquet tables that DuckDB joins on demand. Release id: `ensembl-variation-2026_07_13-vep116.0`. |
|
|
| Built by [prepare-annotations](https://github.com/dna-seq/prepare-annotations) for |
| [just-dna-lite](https://github.com/dna-seq/just-dna-lite). |
|
|
| ## Layout |
|
|
| - `data/homo_sapiens-chr{N}.parquet`: the core, one row per ALT allele: `chrom, start, ref, alt, id, row_idx`. |
| Positions are 1-based VCF POS; REF and ALT are spelled as in the VCF. Same file names and column |
| names as the earlier `just-dna-seq/ensembl_variations` cache, which pipe-joined multi-allelic ALTs |
| into one row; here each ALT has its own row. |
| - `groups/{group}/homo_sapiens-chr{N}.parquet`: sidecar columns keyed by `(chrom, row_idx)`. |
| Sidecars are sparse: an allele with no value in a group has no row there. |
| - `manifest.json`: release id, sources, and every file with its row count, size and SHA-256. |
|
|
| `row_idx` is valid only within one release. Never join files whose `manifest.json` `release_id` differs. |
|
|
| | Group | Default | Rows | Size | Content | Columns | |
| |---|---|---:|---:|---|---| |
| | `core` | yes | 1,391,478,689 | 14.54 GB | Alleles and rsIDs | `chrom`, `start`, `ref`, `alt`, `id`, `row_idx` | |
| | `consequence` | yes | 1,391,478,685 | 4.14 GB | Most severe transcript consequence per allele (by IMPACT, protein-coding first) | `variant_class`, `consequence`, `impact`, `gene_symbol`, `gene_id`, `transcript_id`, `biotype`, `exon`, `intron`, `hgvsc`, `hgvsp`, `amino_acids`, `protein_position`, `sift`, `polyphen` | |
| | `clinical` | yes | 269,631,208 | 0.93 GB | ClinVar significance, PubMed ids and phenotypes Ensembl attaches to the variant | `clin_sig`, `somatic`, `pheno`, `pubmed`, `phenotypes`, `var_synonyms` | |
| | `predictors` | yes | 486,820,688 | 1.63 GB | REVEL, SpliceAI, AlphaMissense, ClinPred and MaveDB (maximum over transcripts) | `revel`, `spliceai_ds_ag`, `spliceai_ds_al`, `spliceai_ds_dg`, `spliceai_ds_dl`, `alphamissense_score`, `alphamissense_class`, `clinpred`, `mavedb_score`, `mavedb_urn` | |
| | `cadd` | optional | 1,323,076,840 | 10.41 GB | CADD v1.7 scores | `cadd_phred`, `cadd_raw` | |
| | `frequency` | yes | 1,359,614,704 | 7.36 GB | Global allele frequencies: gnomAD v4.1 exomes and genomes, 1000 Genomes phase 3 | `af_gnomad_exomes`, `af_gnomad_genomes`, `af_1kg`, `ancestral_allele` | |
| | `frequency_populations` | optional | 755,450,474 | 8.16 GB | Per-population allele frequencies: gnomAD v4.1 exomes and genomes, 1000 Genomes | `af_gnomad_exomes_afr`, `af_gnomad_exomes_amr`, `af_gnomad_exomes_asj`, `af_gnomad_exomes_eas`, `af_gnomad_exomes_fin`, `af_gnomad_exomes_mid`, `af_gnomad_exomes_nfe`, `af_gnomad_exomes_remaining`, `af_gnomad_exomes_sas`, `af_gnomad_genomes_ami`, `af_gnomad_genomes_afr`, `af_gnomad_genomes_amr`, `af_gnomad_genomes_asj`, `af_gnomad_genomes_eas`, `af_gnomad_genomes_fin`, `af_gnomad_genomes_mid`, `af_gnomad_genomes_nfe`, `af_gnomad_genomes_remaining`, `af_gnomad_genomes_sas`, `af_1kg_afr`, `af_1kg_amr`, `af_1kg_eas`, `af_1kg_eur`, `af_1kg_sas` | |
| | `transcripts` | optional | 2,757,116,851 | 4.32 GB | Every GENCODE primary transcript consequence of each allele | `consequence`, `impact`, `gene_symbol`, `gene_id`, `transcript_id`, `biotype`, `exon`, `intron`, `hgvsc`, `hgvsp`, `amino_acids`, `protein_position`, `sift`, `polyphen`, `distance`, `strand` | |
|
|
| ## Querying |
|
|
| Match a sample to the core first, then join only the sidecars you need on `(chrom, row_idx)`: |
|
|
| ```sql |
| WITH m AS ( |
| SELECT v.*, c.row_idx, c.id |
| FROM read_parquet('sample.parquet') v |
| LEFT JOIN read_parquet('data/*.parquet') c USING (chrom, start, ref, alt) |
| ) |
| SELECT m.*, k.* EXCLUDE (chrom, row_idx) |
| FROM m LEFT JOIN read_parquet('groups/consequence/*.parquet') k USING (chrom, row_idx); |
| ``` |
|
|
| ## Sources and licences |
|
|
| - VEP: `##VEP="v116.0" API="v116" time="2026-06-15 16:58:35" cache="/nfs/production/flicek/ensembl/variation/new_website/run_setup/outputs/tmp/homo_sapiens/116_GRCh38" ensembl=116.c0cf13d ensembl-compara=116.46f80af ensembl-funcgen=116.90049ea ensembl-io=116.6afb5dc ensembl-variation=116.2fb834b 1000genomes="phase3" COSMIC="102" ClinVar="202509" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 50" genebuild="GENCODE50" gnomADe="v4.1" gnomADg="v4.1" polyphen="2.2.3" regbuild="1.0" sift="6.2.1"` |
| - CADD: free for non-commercial use only (https://cadd.gs.washington.edu/) |
| - Ensembl data: no restrictions (https://www.ensembl.org/info/about/legal/) |
|
|
| The `cadd` group carries CADD scores, which are free for non-commercial use only; it is a separate |
| group so that commercial users can leave it out. |
|
|
