genome-nexus / genome-nexus-cli

💻 Command line interface for Genome Nexus 🧬

Genome Nexus 🧬

Genome Nexus, 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.

Documentation 📖

See the docs

Run 💻

Alternative 1 - run genome-nexus, mongoDB and genome-nexus-vep in docker containers

First, set environment variables for Ensembl Release, VEP Assembly, location of VEP Cache, and species (since a mouse instalation is supported). If these are not, the default values from .env will be set.

The reference genome and Ensembl release must be consistent with a version in genome-nexus-importer/data/. For example grch37_ensembl92, grch38_ensembl92 or grch38_ensembl95:

export REF_ENSEMBL_VERSION=grch38_ensembl92

If you want to setup Genome Nexus for mouse, also set the SPECIES variable to 'mus_musculus'. Also see the docs to create a mouse database.

export SPECIES=mus_musculus

If you would like to do local VEP annotations instead of using the public Ensembl API, please uncomment # gn_vep.region.url=http://localhost:6060/vep/human/region/VARIANT in your application.properties. This will require you to download the VEP cache files for the preferred Ensembl Release and Reference genome, see our documentation on downloading the Genome Nexus VEP Cache. This will take several hours.

# Set local cache dir
export VEP_CACHE=<local_vep_cache>

# GRCh38 or GRCh37
export VEP_ASSEMBLY=GRCh38

Run docker-compose to create images and containers:

docker-compose up --build -d

Run without recreating images:

docker-compose up -d

Run without Genome Nexus VEP:

# Start both the Web and DB (dependency of Web) containers
docker-compose up -d web

Stop and remove containers:

docker-compose down

Alternative 2 - run genome-nexus locally, but mongoDB in docker container

# the genomenexus/gn-mongo images comes with all the required tables imported
# change latest to different version if necessary (only need to run this once)
docker run --name=gn-mongo --restart=always -p 27017:27017 -d genomenexus/gn-mongo:latest 
mvn  -DskipTests clean install
java -jar web/target/web-*.war

Alternative 3 - install mongoDB locally and run with local java

Install mongoDB manually. Then follow instructions in genome-nexus-importer to initialize the database.

After that run this:

mvn clean install
java -jar web/target/web-*.war

Test Status 👷‍♀️

branch	master	rc
status

Deploy 🚀

genome-nexus-cli's Issues

Using `convert` to convert file.vcf to file.maf returns empty file

Command:

docker run -it --rm node:8.12.0  npx genome-nexus-cli convert file.vcf 

Returns:

npx: installed 86 in 5.465s
Chromosome	Start_Position	End_Position	Reference_Allele	Tumor_Seq_Allele2

Expected:
Variants and annotation values in each of the columns

Example content of vcf file:

chrY	56880089	.	T	C	8	PASS	.	GT:GQ:DP:AD:VAF:PL	0/1:8:3:1,2:0.666667:7,0,31

Variants that are close might be MNV

Check in unfiltered MAF whether two variants are close. Could indicate a MNV

run it with GRCh38

Hi!

There is a beta version built on the GRCh38 in the web interface (mutation_mapper tool), but I can´t find the option to set the reference genome GRCh38 to annotate the MAF files using the command-line interface genome-nexus-cli.
Is there a way to do this?
Thanks