README.md

metadata

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 for 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):

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.