vepyr

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vepyr (/ˈvaɪpər/) — VEP Yielding Performant Results — is a blazing-fast Rust reimplementation of Ensembl's Variant Effect Predictor, exposed as a Python library. It builds and uses Ensembl VEP caches locally, annotates VCF input through a native DataFusion engine, and returns results as a polars.LazyFrame or a VCF with CSQ in the INFO column.

📚 Documentation

https://biodatageeks.org/vepyr/


Quick start	Install, get a cache, annotate
Download Ensembl VEP and plugin caches	Prebuilt release-116 caches
Caches	Cache types, entity schemas, CSQ output fields
Plugins	CADD, SpliceAI, AlphaMissense, ClinVar, dbNSFP
API reference	`build_cache()`, `annotate()`, …
Performance	Benchmarks vs Ensembl VEP

Install

pip install vepyr

See Developers for building from source and running the test suite.

License

Apache-2.0

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0.5.0

Sep 6, 2026 5 files

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0.3.0

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0.2.0

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0.1.1

Jul 5, 2026 5 files

vepyr 0.4.0

vepyr

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