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We will here focus on those end points of the API which are of more interest for HGVA users, giving examples of their use and pin pointing certain peculiarities of the parameters for HGVA. Data is hierarchically organised in Projects and Studies. Please, have a look at Data: sources and HGVA organization in order to understand how data is organized: Projects, Studies and Cohorts . For details on the query parameters, please refer to the Swagger documentation linked above.

Getting information about genomic variants

Getting variant data from a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?studies={project}:{study}

For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will also limit the number of returned results to 3:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?gene=TTN&studies=hgvauser@reference_grch37:GONL&limit=3

Getting information about projects

Getting all metadata from a particular project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/info

For example, getting all metadata for the reference_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/reference_grch37/info

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Getting information about samples

Get all metadata for a particular sample:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/{sample}/info?study={project}:{study}

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http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/GBR/samples?study=reference_grch37:1kG_phase3

Getting information about genomic variants

Getting variant data from a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?studies={project}:{study}

For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will also limit the number of returned results to 3:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?gene=TTN&studies=hgvauser@reference_grch37:GONL&limit=3