# OpenCGA

## v2.2

- [Home](https://docs.opencga.opencb.org/develop-2/readme.md): Welcome to the official page for OpenCGA documentation.
- [Overview](https://docs.opencga.opencb.org/develop-2/overview.md)
- [Features](https://docs.opencga.opencb.org/develop-2/overview/features.md): Overview of main features
- [Architecture Diagram](https://docs.opencga.opencb.org/develop-2/overview/architecture.md)
- [Security](https://docs.opencga.opencb.org/develop-2/overview/security.md)
- [Metadata and Clinical Data](https://docs.opencga.opencb.org/develop-2/overview/data-management.md)
- [Data Models](https://docs.opencga.opencb.org/develop-2/overview/data-models.md)
- [Sample](https://docs.opencga.opencb.org/develop-2/overview/data-models/sample.md)
- [Individual](https://docs.opencga.opencb.org/develop-2/overview/data-models/individual.md)
- [Alignment and Coverage](https://docs.opencga.opencb.org/develop-2/overview/alignment-and-coverage.md)
- [Variant Query and Analysis](https://docs.opencga.opencb.org/develop-2/overview/variant-query-and-analysis.md)
- [Clinical Data Analysis](https://docs.opencga.opencb.org/develop-2/overview/clinical-data-analysis.md)
- [Running Analysis](https://docs.opencga.opencb.org/develop-2/overview/running-analysis.md)
- [Scalability and Performance](https://docs.opencga.opencb.org/develop-2/overview/scalability-and-performance.md)
- [Sizing OpenCGA](https://docs.opencga.opencb.org/develop-2/overview/sizing-opencga.md)
- [OpenCGA Architecture](https://docs.opencga.opencb.org/develop-2/components-1.md)
- [Catalog](https://docs.opencga.opencb.org/develop-2/components-1/catalog.md): Metadata and Clinical Data Database
- [Alignment and Coverage](https://docs.opencga.opencb.org/develop-2/components-1/alignment-and-coverage.md)
- [Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/components-1/variant-storage.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/develop-2/components-1/clinical.md)
- [Analysis Framework](https://docs.opencga.opencb.org/develop-2/components-1/analysis-framework.md)
- [Data Models](https://docs.opencga.opencb.org/develop-2/data-models.md)
- [User](https://docs.opencga.opencb.org/develop-2/data-models/user.md)
- [Project](https://docs.opencga.opencb.org/develop-2/data-models/project.md)
- [Study](https://docs.opencga.opencb.org/develop-2/data-models/study.md)
- [File](https://docs.opencga.opencb.org/develop-2/data-models/file.md)
- [Sample](https://docs.opencga.opencb.org/develop-2/data-models/sample.md)
- [Individual](https://docs.opencga.opencb.org/develop-2/data-models/individual.md)
- [Family](https://docs.opencga.opencb.org/develop-2/data-models/family.md)
- [Cohort](https://docs.opencga.opencb.org/develop-2/data-models/cohort.md)
- [Job](https://docs.opencga.opencb.org/develop-2/data-models/job.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/develop-2/data-models/clinical-analysis.md)
- [Case Studies](https://docs.opencga.opencb.org/develop-2/case-studies.md)
- [Genomics England Research](https://docs.opencga.opencb.org/develop-2/case-studies/genomics-england-research.md)
- [Microsoft Azure](https://docs.opencga.opencb.org/develop-2/case-studies/microsoft-azure.md): Azure HDInisght
- [Installation](https://docs.opencga.opencb.org/develop-2/manual/installation.md)
- [Kubernetes Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes.md)
- [Azure](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/azure.md)
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/configuration.md)
- [On-Premise HPC Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster.md)
- [Server Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/server-configuration.md)
- [Getting OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/building-from-source.md)
- [Choosing Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/chosing-variant-storage.md): HBase vs. MongoDB
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/configuration.md)
- [Running Docker](https://docs.opencga.opencb.org/develop-2/manual/installation/docker.md)
- [Login](https://docs.opencga.opencb.org/develop-2/manual/login.md)
- [Using OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/using-opencga.md): You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started!
- [REST Web Service API](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/restful-web-service-api.md): Understanding REST web service API
- [IVA Web App](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/iva-web-app.md): A rich web app front-end to work with OpenCGA
- [Client Libraries](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries.md): Java, Python, R and Javascript clients are implemented
- [pyopencga - Python Library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/python.md): If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place!
- [opencgaR - R library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/r.md): If you're a R user and you're keen of running OpenCGA through R, you're in the right place!
- [Java](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/java.md)
- [JavaScript](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/javascript.md)
- [Command Line](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line.md)
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/configuration.md)
- [Files](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/files.md): opencga.sh files
- [Public Demo](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/public-demo.md)
- [Managing Data](https://docs.opencga.opencb.org/develop-2/manual/data-management.md)
- [Working with Projects and Studies](https://docs.opencga.opencb.org/develop-2/manual/data-management/projects-and-studies.md)
- [Loading of VCF files](https://docs.opencga.opencb.org/develop-2/manual/data-management/ingestion-of-vcf-files.md): This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store.
- [Working with Files](https://docs.opencga.opencb.org/develop-2/manual/data-management/working-with-files.md)
- [Sharing and Permissions](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions.md)
- [Users and Groups](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/users-and-groups.md)
- [Study ACLs](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/permissions.md)
- [Population of metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata.md)
- [Data Versioning](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/data-versioning.md)
- [Adding Custom Metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/adding-custom-metadata.md)
- [Alignment Engine](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine.md)
- [BAM Index](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/bam-index.md)
- [Alignment Read Query](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-read-query.md)
- [Working with Coverage](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/working-with-coverage.md)
- [Alignment Analysis](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-analysis.md)
- [Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine.md)
- [Variant Query](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-query.md)
- [Variant Aggregation Stats](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-aggregation-stats.md)
- [Variant Analysis](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-analysis.md)
- [Clinical Genomics](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics.md)
- [Clinical Interpretation](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-interpretation.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-analysis.md)
- [Using JupyterLab](https://docs.opencga.opencb.org/develop-2/manual/using-jupyterlab.md)
- [Administrator](https://docs.opencga.opencb.org/develop-2/manual/administrator.md)
- [User Management](https://docs.opencga.opencb.org/develop-2/manual/administrator/user-management.md)
- [Templates / Manifest](https://docs.opencga.opencb.org/develop-2/manual/administrator/templates-manifest.md)
- [Roadmap](https://docs.opencga.opencb.org/develop-2/about/roadmap.md)
- [Release Notes](https://docs.opencga.opencb.org/develop-2/about/release-notes.md)
- [Community](https://docs.opencga.opencb.org/develop-2/about/contributing.md)

## v2.1

- [Home](https://docs.opencga.opencb.org/readme.md): Welcome to the official page for OpenCGA documentation.
- [Overview](https://docs.opencga.opencb.org/overview.md)
- [Features](https://docs.opencga.opencb.org/overview/features.md): Overview of main features
- [Architecture Diagram](https://docs.opencga.opencb.org/overview/architecture.md)
- [Security](https://docs.opencga.opencb.org/overview/security.md)
- [Metadata and Clinical Data](https://docs.opencga.opencb.org/overview/data-management.md)
- [Data Models](https://docs.opencga.opencb.org/overview/data-models.md)
- [Sample](https://docs.opencga.opencb.org/overview/data-models/sample.md)
- [Individual](https://docs.opencga.opencb.org/overview/data-models/individual.md)
- [Alignment and Coverage](https://docs.opencga.opencb.org/overview/alignment-and-coverage.md)
- [Variant Query and Analysis](https://docs.opencga.opencb.org/overview/variant-query-and-analysis.md)
- [Clinical Data Analysis](https://docs.opencga.opencb.org/overview/clinical-data-analysis.md)
- [Running Analysis](https://docs.opencga.opencb.org/overview/running-analysis.md)
- [Scalability and Performance](https://docs.opencga.opencb.org/overview/scalability-and-performance.md)
- [Sizing OpenCGA](https://docs.opencga.opencb.org/overview/sizing-opencga.md)
- [OpenCGA Architecture](https://docs.opencga.opencb.org/components-1.md)
- [Catalog](https://docs.opencga.opencb.org/components-1/catalog.md): Metadata and Clinical Data Database
- [Alignment and Coverage](https://docs.opencga.opencb.org/components-1/alignment-and-coverage.md)
- [Variant Storage Engine](https://docs.opencga.opencb.org/components-1/variant-storage.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/components-1/clinical.md)
- [Analysis Framework](https://docs.opencga.opencb.org/components-1/analysis-framework.md)
- [Data Models](https://docs.opencga.opencb.org/data-models.md)
- [User](https://docs.opencga.opencb.org/data-models/user.md)
- [Project](https://docs.opencga.opencb.org/data-models/project.md)
- [Study](https://docs.opencga.opencb.org/data-models/study.md)
- [File](https://docs.opencga.opencb.org/data-models/file.md)
- [Sample](https://docs.opencga.opencb.org/data-models/sample.md)
- [Individual](https://docs.opencga.opencb.org/data-models/individual.md)
- [Family](https://docs.opencga.opencb.org/data-models/family.md)
- [Cohort](https://docs.opencga.opencb.org/data-models/cohort.md)
- [Job](https://docs.opencga.opencb.org/data-models/job.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/data-models/clinical-analysis.md)
- [Case Studies](https://docs.opencga.opencb.org/case-studies.md)
- [Genomics England Research](https://docs.opencga.opencb.org/case-studies/genomics-england-research.md)
- [Microsoft Azure](https://docs.opencga.opencb.org/case-studies/microsoft-azure.md): Azure HDInisght
- [Installation](https://docs.opencga.opencb.org/manual/installation.md)
- [Kubernetes Cluster](https://docs.opencga.opencb.org/manual/installation/kubernetes.md)
- [Azure](https://docs.opencga.opencb.org/manual/installation/kubernetes/azure.md)
- [Configuration](https://docs.opencga.opencb.org/manual/installation/kubernetes/configuration.md)
- [On-Premise HPC Cluster](https://docs.opencga.opencb.org/manual/installation/compute-cluster.md)
- [Server Configuration](https://docs.opencga.opencb.org/manual/installation/compute-cluster/server-configuration.md)
- [Getting OpenCGA](https://docs.opencga.opencb.org/manual/installation/compute-cluster/building-from-source.md)
- [Choosing Variant Storage Engine](https://docs.opencga.opencb.org/manual/installation/compute-cluster/chosing-variant-storage.md): HBase vs. MongoDB
- [Configuration](https://docs.opencga.opencb.org/manual/installation/compute-cluster/configuration.md)
- [Running Docker](https://docs.opencga.opencb.org/manual/installation/docker.md)
- [Login](https://docs.opencga.opencb.org/manual/login.md)
- [Using OpenCGA](https://docs.opencga.opencb.org/manual/using-opencga.md): You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started!
- [REST Web Service API](https://docs.opencga.opencb.org/manual/using-opencga/restful-web-service-api.md): Understanding REST web service API
- [IVA Web App](https://docs.opencga.opencb.org/manual/using-opencga/iva-web-app.md): A rich web app front-end to work with OpenCGA
- [Client Libraries](https://docs.opencga.opencb.org/manual/using-opencga/client-libraries.md): Java, Python, R and Javascript clients are implemented
- [pyopencga - Python Library](https://docs.opencga.opencb.org/manual/using-opencga/client-libraries/python.md): If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place!
- [opencgaR - R library](https://docs.opencga.opencb.org/manual/using-opencga/client-libraries/r.md): If you're a R user and you're keen of running OpenCGA through R, you're in the right place!
- [Java](https://docs.opencga.opencb.org/manual/using-opencga/client-libraries/java.md)
- [JavaScript](https://docs.opencga.opencb.org/manual/using-opencga/client-libraries/javascript.md)
- [Command Line](https://docs.opencga.opencb.org/manual/using-opencga/command-line.md)
- [Configuration](https://docs.opencga.opencb.org/manual/using-opencga/command-line/configuration.md)
- [Public Demo](https://docs.opencga.opencb.org/manual/using-opencga/public-demo.md)
- [Managing Data](https://docs.opencga.opencb.org/manual/data-management.md)
- [Sharing and Permissions](https://docs.opencga.opencb.org/manual/data-management/sharing-and-permissions.md)
- [Users and Groups](https://docs.opencga.opencb.org/manual/data-management/sharing-and-permissions/users-and-groups.md)
- [Study ACLs](https://docs.opencga.opencb.org/manual/data-management/sharing-and-permissions/permissions.md)
- [Create Projects and Studies](https://docs.opencga.opencb.org/manual/data-management/projects-and-studies.md)
- [Load VCF Files to a Study](https://docs.opencga.opencb.org/manual/data-management/ingestion-of-vcf-files.md): This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store.
- [Working with Files](https://docs.opencga.opencb.org/manual/data-management/working-with-files.md)
- [Population of Metadata](https://docs.opencga.opencb.org/manual/data-management/population-of-metadata.md)
- [Adding Custom Metadata](https://docs.opencga.opencb.org/manual/data-management/population-of-metadata/adding-custom-metadata.md)
- [Data Versioning](https://docs.opencga.opencb.org/manual/data-management/population-of-metadata/data-versioning.md)
- [Alignment Engine](https://docs.opencga.opencb.org/manual/alignment-engine.md)
- [BAM Index](https://docs.opencga.opencb.org/manual/alignment-engine/bam-index.md)
- [Alignment Read Query](https://docs.opencga.opencb.org/manual/alignment-engine/alignment-read-query.md)
- [Working with Coverage](https://docs.opencga.opencb.org/manual/alignment-engine/working-with-coverage.md)
- [Alignment Analysis](https://docs.opencga.opencb.org/manual/alignment-engine/alignment-analysis.md)
- [Variant Storage Engine](https://docs.opencga.opencb.org/manual/variant-storage-engine.md)
- [Variant Query](https://docs.opencga.opencb.org/manual/variant-storage-engine/variant-query.md)
- [Variant Aggregation Stats](https://docs.opencga.opencb.org/manual/variant-storage-engine/variant-aggregation-stats.md)
- [Variant Analysis](https://docs.opencga.opencb.org/manual/variant-storage-engine/variant-analysis.md)
- [Clinical Genomics](https://docs.opencga.opencb.org/manual/clinical-genomics.md)
- [Clinical Interpretation](https://docs.opencga.opencb.org/manual/clinical-genomics/clinical-interpretation.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/manual/clinical-genomics/clinical-analysis.md)
- [Using JupyterLab](https://docs.opencga.opencb.org/manual/using-jupyterlab.md)
- [Administrator](https://docs.opencga.opencb.org/manual/administrator.md)
- [User Management](https://docs.opencga.opencb.org/manual/administrator/user-management.md)
- [Templates / Manifest](https://docs.opencga.opencb.org/manual/administrator/templates-manifest.md)
- [Roadmap](https://docs.opencga.opencb.org/about/roadmap.md)
- [Release Notes](https://docs.opencga.opencb.org/about/release-notes.md)
- [Community](https://docs.opencga.opencb.org/about/contributing.md)