vepyr
vepyr (/ˈvaɪpər/) — VEP Yielding Performant Results — is a blazing-fast Rust
reimplementation of Ensembl's Variant Effect
Predictor, exposed as a
Python library and a vepyr command. 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 |
| Polars DataFrames | Schema, region filters, filter_vep in Polars |
| Command line | vepyr annotate, VCF in, VCF out |
| Nextflow | The vepyr/annotate module, amd64 and arm64 containers, and the vcf_annotate_vepyr subworkflow (normalize, optional Hugging Face 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, PhenotypeOrthologous |
| API reference | build_cache(), annotate(), … |
| Performance | Benchmarks vs Ensembl VEP |
Install
pip install vepyr
or from bioconda (linux-64, osx-64, osx-arm64):
conda install -c conda-forge -c bioconda vepyr
Either installs both the Python package and a vepyr executable:
vepyr annotate \
-i input.vcf.gz \
-o annotated.vcf.gz \
--dir_cache ~/vepyr_cache/116_GRCh38_ensembl \
--fasta GRCh38.fa \
--fork 8
See Developers for building from source and running the test suite.
License
1 maintainer
Metadata
1 maintainer
Release files for vepyr 0.9.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| vepyr-0.9.2.tar.gz | 13.0 MB | With provenance | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| vepyr-0.9.2-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| vepyr-0.9.2-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| vepyr-0.9.2-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| vepyr-0.9.2-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
| vepyr-0.9.2-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 308.1 MB
Release files / vepyr-0.9.2.tar.gz
| Download URL | vepyr-0.9.2.tar.gz |
|---|---|
| Size | 13.0 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f76c8eabe8db57ddbdef6459f9b1d493502188c7967121db8fa0c81a886d1d4e
|
|
BLAKE2b-256 checksum How to use checksums |
8519d9af3466e523c74f31ce5204185e63645e709f1fa89e32e6f599b5838792
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logRelease files / vepyr-0.9.2-cp310-abi3-win_amd64.whl
| Download URL | vepyr-0.9.2-cp310-abi3-win_amd64.whl |
|---|---|
| Size | 55.5 MB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
17159722335688001e12cd3998e4d2ea939f25a87f8d3bb61f4d4f7e705f845d
|
|
BLAKE2b-256 checksum How to use checksums |
ca07bdec757c443392fd7756e17fd0beb54b7cd51098cd154a110e60b3048651
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logRelease files / vepyr-0.9.2-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vepyr-0.9.2-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 62.7 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
97f7391f980f33ff9a4357c5e36f9b4432d8505b839a8b8948e2a1389c8abcda
|
|
BLAKE2b-256 checksum How to use checksums |
410476a99e2ac983463003fc69fcc93001f6c9ded88f4f69d1a7a66887ec3446
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logRelease files / vepyr-0.9.2-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | vepyr-0.9.2-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 61.5 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 abi3 |
|
SHA-256 checksum How to use checksums |
9d1b1b97517f209d3816ecc4440e5b84860f59235d3a3b6e7fd4a2e9f30f45ca
|
|
BLAKE2b-256 checksum How to use checksums |
85fd0f46b98f4f12fc662c514310f73099fef8e5aa768a9df949f95ef6c0b748
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logRelease files / vepyr-0.9.2-cp310-abi3-macosx_11_0_arm64.whl
| Download URL | vepyr-0.9.2-cp310-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 56.3 MB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
217402ed1d2483c2625cda7d33ad2ca3bc56dd45e77d6a4621377988ce2206ef
|
|
BLAKE2b-256 checksum How to use checksums |
54d7442452d66c2bf5f68c1e3e2f670e74c15a07914e2d1fda3734850aa80573
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logRelease files / vepyr-0.9.2-cp310-abi3-macosx_10_12_x86_64.whl
| Download URL | vepyr-0.9.2-cp310-abi3-macosx_10_12_x86_64.whl |
|---|---|
| Size | 59.1 MB |
| Tags | CPython 3.10 abi3 macOS 10.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
4c36f2447e48ed5042243e6fa59c9de19a169ecf67ddddf492238d79b94855a3
|
|
BLAKE2b-256 checksum How to use checksums |
213a2fd0092dd8f75795a75af8a432e883949de47b9dd56481c90374f8ee67a5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logSecurity for vepyr 0.9.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 6 files in this release have been uploaded with provenance metadata.
Attestation for vepyr-0.9.2.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 9, 2026.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
