genome-nexus-cli
v0.0.14
Published
Genome Nexus Command Line Interface
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Command Line Interface for Genome Nexus
Genome Nexus is a web service: https://www.genomenexus.org. A comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus integrates information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability. For a list of all annotations see here: https://docs.genomenexus.org/annotation-sources. This command line client annotates VCF and MAF files using annotations provided by the Genome Nexus API. The command line client's internal logic is lean: it sends a HTTP request to the Genome Nexus REST API to retreive annotations. Most logic happens in the web service itself. The variants are sent without sample IDs, so the variants can't be related back to specific samples.
Install 💻
For users
Genome Nexus can be installed/run in several ways, choose which one works for you:
- If you have npm installed. You can run it directly with:
or install globally with:npx genome-nexus-cli --help
npm install -g genome-nexus-cli genome-nexus --help
- If you have Docker installed:
docker run -it --rm node:8.12.0 npx genome-nexus-cli --help
- If you have conda installed:
conda create -c conda-forge -n genome-nexus-env nodejs conda activate genome-nexus-env npm install -g genome-nexus-cli genome-nexus --help
If you use none of these and prefer another way of installing please file a request in the issue tracker: https://github.com/genome-nexus/genome-nexus-cli/issues.
For developers
git clone https://github.com/genome-nexus/genome-nexus-cli
yarn
yarn build
yarn link
Usage examples 🧬
Check the help docs:
genome-nexus --help
Convert VCF to MAF ready for annotation
genome-nexus convert variants.vcf
Annotate maf file
Given input MAF file like: test/data/minimal_example.in.txt. Get annotated output MAF like: test/data/minimal_example.out.txt
genome-nexus annotate maf test/data/minimal_example.in.txt > test/data/minimal_example.out.txt
Note that there is also a web interface to do this: https://www.cbioportal.org/mutation_mapper.
Include OncoKB annotations
To add OncoKB annotations one should first obtain a license. Once you have a token one can add oncokb annotations like this:
genome-nexus annotate maf --tokens {"oncokb":"xxx-xxx-xxxx"} test/data/minimal_example.in.txt > test/data/minimal_example.out.txt
Get JSON output for a single variant
genome-nexus annotate variant 17:g.41242962_41242963insGA
Gives raw JSON output: https://www.genomenexus.org/annotation/17:g.41242962_41242963insGA
TODO 🔧
- [ ] Output ignored variants instead of only failed variants. E.g. when genomic location is not valid
- [ ] Add tests for
- [ ] single variant anntotation
- [ ] maf annotation
- [ ] vcf conversion
- [ ] There are still many more annotation sources to add: https://docs.genomenexus.org/annotation-sources