BIPMed Variant Explorer

This is the reference implementation server of the Brave API. It accepts Query as POST request and returns a list of Variant.

Query

• variantId - Unique identifier (rs6054257)
• assemblyId - Version of reference genomes (GCRh38, null for all reference genomes)
• datasetId - Dataset id (bipmedExome, null for all datasets)
• referenceName - Chromosome (20, must be present when geneSymbol is null)
• start - Exact position when end is null, otherwise is start (include) of range (1000, must be present)
• end - End (include) of range (must be present when start is not null)
• geneSymbol - Gene Symbol (SCN1A, it can be combined with referenceGenome, start and end)

Variant

• variantIds - List of unique identifiers where available, can be null (ID)
• assemblyId - Version of reference genome, required
• datasetId - Dataset id, required
• referenceName - An identifier from the reference genome, required (CHROM)
• start - The reference position, with the 1st base having position 1, required (POS)
• referenceBases - Reference bases, required (REF)
• alternateBases - List of alternate non-reference alleles, required (ALT)
• geneSymbol - Gene symbol, can be null
• alleleFrequency - Allele Frequency, required (AF)
• sampleCount - Number of Samples With Data, required (NS)

Environment variables

Server specific.

• BRAVE_DATABASE URL to Mongo database. Default is mongodb://localhost:27017.
• BRAVE_ADDRESS address to bind server. Default is :8080.
• BRAVE_USERNAME administrator user name. Default is admin.
• BRAVE_PASSWORD administrator password. Default is empty.

Deploy server with Docker

Create network and volume.

docker volume create brave-data
docker network create brave

docker container run \
    --network brave \
    --rm --detach \
    --name brave-db \
    --volume brave-data:/data/db \
    mongo:4

docker container run \
    --rm --detach \
    --name brave \
    --network brave \
    --publish 8080:8080 \
    --env BRAVE_DATABASE=mongodb://brave2-db:27017 \
    --env BRAVE_PASSWORD=secret \
    bipmed/brave server

Import variants

BraVE accepts VCF files (v4.2) as input and submit variants to server instance. No genotype (FORMAT column) data is sent to server. FORMAT/DP and FORMAT/GQ are used to calculate distribution (min, q25, median, q75, max and average) of every variant. By default only variant that passed all filters are imported to database (FILTER = PASS or .). Use --dont-filter option to import all variants, regardless of FILTER column.

brave import \
    [--dont-filter] \
    [--dry-run] \
    [--host http://localhost:8080] \
    [--username admin] \
    --password secret \
    --assembly hg38 \
    --dataset bipmed \
    bipmed.hg38.vcf.gz