As described in the documentation, HGVA backend is powered by the OpenCGA project. The CLI is distributed with the rest of the OpenCGA code. The OpenCGA code can be cloned in your machine by executing in your terminal. Checkout the latest code (release-1.1.0 branch):
$ git clone https://github.com/opencb/opencga.git $ git checkout v1.3.6
Alternatively, you can download tar.gz files with the code for the latest tags/releases of OpenCGA from:
Once you have downloaded the code, follow the instructions at the How to Build section of the OpenCGA repository:
The CLI interface is accessible through the opencga.sh script:
cd opencga cd build cd bin opencga/build/bin$ ./opencga.sh Program: OpenCGA (OpenCB) Version: 1.1.0 Git commit: f2dace56fcdf491efee8ebb0cb43f981e31c320e Description: Big Data platform for processing and analysing NGS data Usage: opencga.sh [-h|--help] [--version] <command> [options] Catalog commands: users User commands projects Project commands studies Study commands files File commands jobs Jobs commands individuals Individual commands families Family commands samples Samples commands variables Variable set commands cohorts Cohorts commands Analysis commands: alignments Implement several tools for the genomic alignment analysis variant Variant commands
The CLI provides commands, subcommands and parameters to access its functionality. Commands of most interest for HGVA users are projects, studies, cohorts and samples. Please, find below a list of commands which can be of most interest for HGVA user. Further documentation on the OpenCGA CLI can be found at the Command Lines section of the OpenCGA documentation.
As previously said, the CLI makes intensive use of the RESTful API. Thus, the only configuration detail needed for the CLI to work is a URL where the Web Services API is hosted. The configuration file client-configuration.yml is used for this purpose. You shall find a template of this file at the build/conf directory:
$ ll opencga/build/conf/client-configuration.yml -rw-r--r-- 1 fjlopez fjlopez 290 Oct 24 17:49 opencga/build/conf/client-configuration.yml
Edit this file with any text editor and set the rest → host attribute to "http://bioinfo.hpc.cam.ac.uk/hgva":
--- ## number of seconds that session remain open sessionDuration: 12000 ## REST client configuration options rest: host: "http://bioinfo.hpc.cam.ac.uk/hgva" batchQuerySize: 200 timeout: 30000 defaultLimit: 2000 ## gRPC configuration options grpc: host: "localhost:9091"
You can query variants by using the variant command and query subcommand. An extensive list of filtering parameters allow great flexibility on the queries. Please, check inline help provided by opencga.sh for further details. For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will restrict studies data to those corresponding to GONL. Finally, we will also limit the number of returned results to 3:
./opencga.sh variant query --gene TTN --study GONL --limit 3 --of json --output-study GONL
You can use the command projects to query projects data.
For getting all metadata from a particular project you can use the info subcommand. For example, getting all metadata for the cancer_grch37 project:
./opencga.sh projects info --project cancer_grch37
For getting all metadata from all studies associated to a particular project yo ucan use the studies subcommand. For example, getting all studies and their metadata for the cancer_grch37 project:
./opencga.sh projects studies --project cancer_grch37
You can use the command studies to query studies data.
For getting all available studies and their metadata you can use the search subcommand. For example, getting all metadata for all available studies (please note, of special interest will be here the field alias which contains the study identifier to be used as an input whenever a study must be passed as a parameter):
./opencga.sh studies search
For getting summary data from a particular study you can use the summary subcommand. For example, getting summary data for study 1kG_phase3 which is framed within project reference_grch37:
./opencga.sh studies summary --study reference_grch37:1kG_phase3
For getting all available metadata for a particular study you can use the info command. For example, getting all metadata for study GONL which is framed within the project reference_grch37:
./opencga.sh studies info --study GONL
For getting all samples metadata for a given study you can use the samples subcommand. For example, getting all samples metadata for study 1kG_phase3 which is framed within project reference_grch37. Please, note that not all studies contain samples data, e.g. GONL, ExAC, among others, only provide variant lists and aggregated frequencies, i.e. no sample genotypes.
./opencga.sh studies samples --study reference_grch37:1kG_phase3
For getting all metadata for a particular sample you can use the info subcommand. For example, get all metadata for sample HG00096 of the 1kG_phase3 study which is framed within the reference_grch37 project:
./opencga.sh samples info --sample HG00096 --study reference_grch37:1kG_phase3
For getting all samples metadata in a given cohort you can use the samples subcommand. For example, get all samples metadata for cohort GBR from study 1kG_phase3 which is framed within project reference_grch37:
./opencga.sh cohorts samples --study reference_grch37:1kG_phase3 --cohort GBR
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