This Python package is designed to process Variant Call Format (VCF) files and perform lookup operations on Genomic Variation Representation Service (GA4GH VRS) identifiers. The GA4GH VRS identifiers provide a standardized way to represent genomic variations, making it easier to exchange and share genomic information.
In addition, this project facilitates the retrieval of evidence associated with genomic alleles by leveraging the Genomic Data Representation and Knowledge Base (GA4GH MetaKB) service. GA4GH MetaKB provides a comprehensive knowledge base that links genomic variants to relevant clinical variant interpretations.
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VCF File Processing:
- Streamlines reading and parsing of VCF files, to extract relevant genomic information.
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GA4GH VRS Identifier Lookup:
- Utilizes the GA4GH VRS API to perform lookups for each genomic variation mentioned in the VCF file.
- Retrieves standardized identifiers for the alleles, enhancing interoperability with GA4GH-compliant systems.
- GA4GH MetaKB Service Integration: Utilizes the GA4GH MetaKB retrieve evidence associated with specified genomic alleles.
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Output Generation:
- Generates summary metrics about throughput, errors, evidence, and hits.
- Presents the retrieved evidence in a structured format, providing access to information about studies, publications, and other relevant details.
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Additional Features
- Provides configurable options like threading and caching for processing VCFs.
- Implements robust error handling to address issues like invalid input files, invalid variants, and more.
- Python 3.10 or later
- Internet connectivity for dependency setup (seqrepo)
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Clone the repository:
git clone https://github.com/ohsu-comp-bio/vrs_anvil_toolkit cd vrs_anvil_toolkit -
Install dependencies:
- for local use
# install postgresql@14 (required for vrs-python) brew install postgresql@14 bash scripts/setup.sh- for use on Terra
bash terra/setup.sh
Manifest
The configuration is controlled by a manifest.yaml file. This manifest file specifies the input VCF file(s), the output directory, and other configurations.
CLI
source venv/bin/activate
# navigate to a working directory, with your manifest.yaml file. Add the VCF urls or file paths to your manifest
# run the vrs_bulk command in the foreground
vrs_bulk annotate
# run the vrs_bulk command in parallel, one process per VCF file
vrs_bulk annotate --scatter
# run the vrs_bulk command in parallel in the background
nohup vrs_bulk annotate --scatter & # press enter to continue
# get the status of the scatter processes
vrs_bulk psProcessing VCF Files (vrs-python)
vrs-python is a GA4GH GKS package centered around creating Variant Representation specification (VRS) IDs: consistent, globally unique identifiers for variation. Some of its functionality includes variant ID translation and VCF annotation. Used as a dependency in vrs_bulk, it can also be used as a standalone package.
For Python usage, see vrs_vcf_annotator.py for an example.
For CLI usage:
python3 -m ga4gh.vrs.extras.vcf_annotation --vcf_in tests/fixtures/1kGP.chr1.1000.vcf --vcf_out annotated_output.vcf.gz --vrs_pickle_out allele_dicts.pkl --seqrepo_root_dir ~/seqrepo/latestThe above is an example using an example vcf. Replace the --vcf_out and vrs_pickle_out here with your desired output file path, where the output vcf can be BCF (vcf.gz) or VCF (vcf)
Terra
The command line utility supports Google Cloud URIs and running commands in the background to interop with Terra out-of-the-box. This is described in the CLI usage above. For an example notebook, see vrs-anvil-demo.ipynb on the vrs-anvil workspace.
This project is open to contributions from the research community. If you are interested in contributing to the project, please contact the project team. See the contributing guide for more information on how to contribute to the project.
This project is licensed under the MIT License - see the LICENSE file for details.