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 0.9.1
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-0.9.1.tar.gz | 13.0 MB | With provenance | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| vepyr-0.9.1-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| vepyr-0.9.1-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| vepyr-0.9.1-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| vepyr-0.9.1-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
| vepyr-0.9.1-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-0.9.1.tar.gz
| Download URL | vepyr-0.9.1.tar.gz |
|---|---|
| Size | 13.0 MB |
| Tags | Source |
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| Download URL | vepyr-0.9.1-cp310-abi3-win_amd64.whl |
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| Size | 55.5 MB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
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|---|---|
| Size | 62.7 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 abi3 |
|
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| Size | 61.5 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 abi3 |
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|---|---|
| Size | 56.3 MB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
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| Size | 59.1 MB |
| Tags | CPython 3.10 abi3 macOS 10.12+ x86-64 |
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