vepyr

VEP Yielding Performant Results — a blazing-fast Rust reimplementation of Ensembl's Variant Effect Predictor.

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What is vepyr?

vepyr is a Python library backed by a native Rust engine that provides:

• Cache conversion — download and convert Ensembl VEP offline caches to an optimized partitioned Parquet cache
• Variant annotation — annotate VCF files with transcript consequences, HGVS notation, allele frequencies, and more
• Full --everything parity — aims for zero mismatches against Ensembl VEP for the supported scope
• 50x+ speedup — dramatically faster than the reference Perl implementation

Key features

• Python-first API — two functions: build_cache() and annotate()
• Polars integration — annotation results returned as polars.LazyFrame for efficient downstream analysis
• VCF output — write annotated VCFs with CSQ in the INFO column, compatible with downstream tools
• Streaming engine — built on Apache Arrow and DataFusion for memory-efficient processing of large datasets
• Point-lookup Parquet cache — partitioned, page-indexed Parquet shards for fast co-located variant lookups

Supported scope

Parameter	Value
Species	homo_sapiens
Assembly	GRCh38
Cache types	ensembl, merged, refseq
Ensembl releases	115+
Python	3.10 — 3.14
Platforms	Linux (x86_64), macOS (x86_64, aarch64)

Quick example

import vepyr

# Build cache from a local Ensembl VEP offline cache
results = vepyr.build_cache(
    release=115,
    cache_dir="/data/vepyr_cache",
    cache_type="ensembl",
    local_cache="/data/ensembl_vep/homo_sapiens/115_GRCh38",
)

# Annotate variants
lf = vepyr.annotate(
    vcf="input.vcf.gz",
    cache_dir="/data/vepyr_cache/parquet/115_GRCh38_ensembl",
    everything=True,
    reference_fasta="GRCh38.fa",
)

df = lf.collect()
print(df.select("chrom", "start", "ref", "alt", "SYMBOL", "Consequence", "IMPACT"))