VCFcache cache gnomAD v4.1 joint GRCh38 (AF ≥ 0.01) annotated with vep 115.2 -e

Abstract VCFcache cache derived from gnomAD v4.1 joint frequency data (GRCh38). Annotation tool: Ensembl VEP 115.2 (via Apptainer). Includes Comprehensive annotation (–everything), HGVS nomenclature (–hgvsg).

Note This upload includes both the annotation cache and its underlying blueprint. The blueprint can be used to build new caches with different annotation recipes.

Contents This underlying blueprint contains 19M high-quality variant sites filtered to allele frequency (AF) ≥ 0.01 (1% or 1 in 100 individuals). All genotype and INFO fields have been removed, retaining only genomic positions (CHROM, POS, REF, ALT). Multiallelic sites have been split into separate records.

Technical details
Coverage: chr1-22, chrX, chrY
Source: gnomAD v4.1.0 joint frequency (807,162 samples)
Processing: AF-filtered (≥10%), normalized, GT/INFO removed, multiallelics split, vep annotated
Annotation tool: Ensembl VEP 115.2
VEP cache: Ensembl 115, GRCh38

VEP Annotations Included (CSQ INFO field)
Comprehensive annotation (–everything)
HGVS nomenclature (–hgvsg)

Setup: vcfcache cache-build --doi <DOI>

Usage: vcfcache annotate -a <cache_dir> -i sample.vcf.gz -o sample_vc.bcf --stats-dir output/

Documentation: VCFcache wiki