Command Line Interface for GeneBe -- The Genetic Variant Interpretation Tool
genebe-cli is a client application for accessing the GeneBe API, a comprehensive tool for genetic variant interpretation. GeneBe aggregates data from various reputable sources, providing essential variant information, including variant function, GnomAD frequencies, and ClinVar annotations. Additionally, GeneBe offers an ACMG variant pathogenicity calculator to aid in variant assessment. For more information, visit GeneBe.
- VCF File Annotation: genebe-cli enables quick and straightforward annotation of VCF files, making variant interpretation easier for researchers.
- Automatic Liftover: Seamlessly performs coordinate liftover between genome builds.
- Multiallelic Splitting: Automatically splits multiallelic VCF entries into single-allelic records.
- Variant Type Support: Currently supports only SNVs (Single Nucleotide Variants) and small InDels. Structural Variants (SV) and Copy Number Variants (CNV) are not yet supported.
- GeneBeHub Client: use GeneBe Hub, push, pull and create new variant annotations that can be easily applied to your VCF
Comprehensive documentation and usage examples can be found at GeneBe VCF File Annotation Guide.
This is experimental:
If you use docker, it may be wise to create and mount the $HOME, to let genebe create the ~/.genebe folder, or create it by hand and mount.
docker run -it --rm --user $(id -u):$(id -g) -v ${HOME}:/home/$(whoami) -v $(pwd):/workspace -w /workspace ghcr.io/pstawinski/genebe-cli:latestgenebe-cli is free to use for research purposes. It is also Research Use Only. Please note that the tool is currently in alpha, so feedback and issue reports are encouraged to help improve its functionality. If you encounter any issues or have suggestions, please raise them in the GitHub Issues section.
Developed with love in Poland 💙