WARNING ⚠️: The java based MAF annotator and associated vcf2maf python conversion scripts are more up to date, use this at your own risk. This was an attempt to restructure the cli interface but it is not actively maintained.

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:

  npx genome-nexus-cli --help
  

  or install globally with:

  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

Test Status 👷‍♀️

branch	master
status