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USAGE.md

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Usage

Quick Start

Stable releases of the Variantstore are bundled as an executable jar and can be downloaded from Releases. See INSTALLATION for more information.

Please make sure that the required environment variables are set accordingly as described in CONFIGURATION.

Import variants

Variants can be imported to the store by using a POST request to the corresponding /variants endpoint. The variants have to be associated with metadata and the following properties have to be specified in JSON schema.

"case": {"identifier": "string"} "variant_annotation": {"version": "string", "name": "string", "doi": "string"}, "variant_calling": {"version": "string", "name": "string", "doi": "string"}, "reference_genome": {"source": "string", "version": "string", "build": "string"}, "is_somatic": "boolean", "samples": [{"identifier": "string", "cancerEntity": "string"}]

For example using curl your upload command would look like this:

curl -X 'POST' \
'${host}:${variantstore-port}/variants' \
-H 'accept: application/json' \
-H 'Content-Type: multipart/form-data' \
-F metadata='{"case": {"identifier": "do1234"}, "variant_annotation": {"version": "bioconda::4.3.1t", "name": "snpeff", "doi": "10.4161/fly.19695"}, "is_somatic": "true", "samples": [{"identifier": "S123456", "cancerEntity": "HCC"}], "reference_genome": {"source": "GATK", "version": "unknown", "build": "hg38"}, "variant_calling": {"version": "bioconda::2.9.10", "name": "Strelka", "doi": "10.1038/s41592-018-0051-x"}}' \
-F files=@/path/to/variants.vcf.gz

Import additional gene information

Information on genes, such as biotype, name, and description, can be imported to the store in gff3 format.

For example using curl your upload command would look like this:

curl -X 'POST' \
'${host}:${variantstore-port}'/genes' \
-H 'accept: application/json' \
-H 'Content-Type: multipart/form-data' \
-F 'files=@/path/to/genes.GRCh38.87.gff3'

This feature is currently supported for gff3 files derived from Ensembl. The Ensembl version (87 in the example above) is expected to be part of the file name otherwise the corresponding database field will be empty.

Retrieve data from the store

Stored data can be retrieved from the store by sending HTTP GET requests.

For example if you want to get a variant from the store at a specific genomic position using curl your command would look like this:

curl '${host}:${variantstore-port}'/variants?startPosition=22310284'

The full list of available endpoints can be seen below.

REST API

The detailed documentation of the REST endpoints provided by the Variantstore can be found on SwaggerHub. Additionally, views for the generated OpenAPI specification are generated as swagger-ui and rapidoc views. After startup, these views are accessible via /swagger-ui and /rapidoc.

GET /genes/{id}
Request a gene
GET /genes
Request a set of genes
POST /genes
Upload gene information
GET /variants/{id}
Request a variant
GET /variants
Request a set of variants
POST /variants
Add variants to the store
GET /variants/upload/status/{id}
Request the variant upload status
GET /cases/{id}
Request a case
GET /cases
Request a set of cases
GET /samples/{id}
Request a sample
GET /samples
Request a set of samples
GET /beacon/query
Query the beacon for a variant

Built-in Endpoints

GET /health
Status of the Variantstore service
GET /swagger-ui
OpenAPI documentation in swagger-ui format
GET /rapidoc
OpenAPI documentation in rapidoc format