{"version":1,"pages":[{"id":"-MHDrXvrawJl4gZ11rNo","title":"Home","pathname":"/develop-2","siteSpaceId":"sitesp_rfm3A","description":"Welcome to the official page for OpenCGA documentation."},{"id":"-MHECj6Xj1FnH4Ewr2lf","title":"Overview","pathname":"/develop-2/overview","siteSpaceId":"sitesp_rfm3A","description":""},{"id":"-MQ4hWiST7q9m8cajxqL","title":"Features","pathname":"/develop-2/overview/features","siteSpaceId":"sitesp_rfm3A","description":"Overview of main features","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWiTfA8bmBUCgyR6","title":"Architecture Diagram","pathname":"/develop-2/overview/architecture","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWiUDgaQ_Ktk0P18","title":"Security","pathname":"/develop-2/overview/security","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWiVlxjTkaV3gPu-","title":"Metadata and Clinical Data","pathname":"/develop-2/overview/data-management","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MiWZPT8bscjXa3Xep4U","title":"Data Models","pathname":"/develop-2/overview/data-models","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MiWZPT978z832nk2NTL","title":"Sample","pathname":"/develop-2/overview/data-models/sample","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"},{"label":"Data Models"}]},{"id":"-MiWZPTApRo2U60LHxpw","title":"Individual","pathname":"/develop-2/overview/data-models/individual","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"},{"label":"Data Models"}]},{"id":"-MQ4hWiZuRMuuFj1uWlE","title":"Alignment and Coverage","pathname":"/develop-2/overview/alignment-and-coverage","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWi_9SzNnULCybTg","title":"Variant Query and Analysis","pathname":"/develop-2/overview/variant-query-and-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWian1yscq183UrD","title":"Clinical Data Analysis","pathname":"/develop-2/overview/clinical-data-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWib9g7o-QcwAaFv","title":"Running Analysis","pathname":"/develop-2/overview/running-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWicyULOTBuYywXB","title":"Scalability and Performance","pathname":"/develop-2/overview/scalability-and-performance","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWiez4H7IJf051jZ","title":"Sizing OpenCGA","pathname":"/develop-2/overview/sizing-opencga","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MQ4hWihDb267LffDca-","title":"OpenCGA Architecture","pathname":"/develop-2/components-1","siteSpaceId":"sitesp_rfm3A","description":""},{"id":"-MQ4hWiiqbKsWZkQgmjG","title":"Catalog","pathname":"/develop-2/components-1/catalog","siteSpaceId":"sitesp_rfm3A","description":"Metadata and Clinical Data Database","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDwqxCbxOY-lD7i5Uo","title":"Alignment and Coverage","pathname":"/develop-2/components-1/alignment-and-coverage","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDuare_SumKP8IACv3","title":"Variant Storage Engine","pathname":"/develop-2/components-1/variant-storage","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MlPjWbU-dyz603tCEcT","title":"Clinical Analysis","pathname":"/develop-2/components-1/clinical","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDwNNkV4gGTqUn9fbx","title":"Analysis Framework","pathname":"/develop-2/components-1/analysis-framework","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MiWZPTPKpLcL21qZqh-","title":"Data Models","pathname":"/develop-2/data-models","siteSpaceId":"sitesp_rfm3A","description":""},{"id":"-MiWZPTQyqkzGO7vSmY2","title":"User","pathname":"/develop-2/data-models/user","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTRGOn7CiBlq5gs","title":"Project","pathname":"/develop-2/data-models/project","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTSEwkFybVOOJNc","title":"Study","pathname":"/develop-2/data-models/study","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTTXYMMJtK2GDvt","title":"File","pathname":"/develop-2/data-models/file","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTUjtdzsFDxGSmn","title":"Sample","pathname":"/develop-2/data-models/sample","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTVa2_DVGCNKUHr","title":"Individual","pathname":"/develop-2/data-models/individual","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTWKHU-Z1uSkT3p","title":"Family","pathname":"/develop-2/data-models/family","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTX3BTB4LUJacCy","title":"Cohort","pathname":"/develop-2/data-models/cohort","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MiWZPTYOAF1vZbmX5J1","title":"Job","pathname":"/develop-2/data-models/job","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"dVFSsYnW4YIGy5thruFr","title":"Clinical Analysis","pathname":"/develop-2/data-models/clinical-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MHDxqjggzacPuAiMMi7","title":"Case Studies","pathname":"/develop-2/case-studies","siteSpaceId":"sitesp_rfm3A","description":""},{"id":"-MHDxx8km4oR423iZ_so","title":"Genomics England Research","pathname":"/develop-2/case-studies/genomics-england-research","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"Case Studies"}]},{"id":"-MHDy5GJaAwAd3o2X47D","title":"Microsoft Azure","pathname":"/develop-2/case-studies/microsoft-azure","siteSpaceId":"sitesp_rfm3A","description":"Azure HDInisght","breadcrumbs":[{"label":"Case Studies"}]},{"id":"-MHDtC51-Gdzm_1m6XtR","title":"Installation","pathname":"/develop-2/manual/installation","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDrtMRS4G4Z5Esr1Mz","title":"Kubernetes Cluster","pathname":"/develop-2/manual/installation/kubernetes","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MHDsBAq2SOy8Vls3UyS","title":"Azure","pathname":"/develop-2/manual/installation/kubernetes/azure","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"Kubernetes Cluster"}]},{"id":"-MMVNBZNSDwutdk1cFLt","title":"Configuration","pathname":"/develop-2/manual/installation/kubernetes/configuration","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"Kubernetes Cluster"}]},{"id":"-MHDryfAb6qrpYJfb19y","title":"On-Premise HPC Cluster","pathname":"/develop-2/manual/installation/compute-cluster","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MHDsG2-eQLC3RiStR5S","title":"Server Configuration","pathname":"/develop-2/manual/installation/compute-cluster/server-configuration","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MMVNBZQAOnin_rVwMgc","title":"Getting OpenCGA","pathname":"/develop-2/manual/installation/compute-cluster/building-from-source","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MMVNBZRlgQO4DJKvhFS","title":"Choosing Variant Storage Engine","pathname":"/develop-2/manual/installation/compute-cluster/chosing-variant-storage","siteSpaceId":"sitesp_rfm3A","description":"HBase vs. MongoDB","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MNBs-Mg7PEFTYRC51yx","title":"Configuration","pathname":"/develop-2/manual/installation/compute-cluster/configuration","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MHDrhJgw20RM4PEKcIM","title":"Running Docker","pathname":"/develop-2/manual/installation/docker","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MiWZPToeQsEcKDzJFnx","title":"Login","pathname":"/develop-2/manual/login","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDtwi8Qn-RqZ1VfF9-","title":"Using OpenCGA","pathname":"/develop-2/manual/using-opencga","siteSpaceId":"sitesp_rfm3A","description":"You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started!","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDuPyYw1eYfH7fKQLM","title":"REST Web Service API","pathname":"/develop-2/manual/using-opencga/restful-web-service-api","siteSpaceId":"sitesp_rfm3A","description":"Understanding REST web service API","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MQ4hWj0h37P9ELLkH6I","title":"IVA Web App","pathname":"/develop-2/manual/using-opencga/iva-web-app","siteSpaceId":"sitesp_rfm3A","description":"A rich web app front-end to work with OpenCGA","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MQ4hWj1FjR94_AvfAlq","title":"Client Libraries","pathname":"/develop-2/manual/using-opencga/client-libraries","siteSpaceId":"sitesp_rfm3A","description":"Java, Python, R and Javascript clients are implemented","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MQ4hWj3tvicxhxPBDjE","title":"pyopencga - Python Library","pathname":"/develop-2/manual/using-opencga/client-libraries/python","siteSpaceId":"sitesp_rfm3A","description":"If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place!","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MQ4hWj4OQLBHyNYjQwF","title":"opencgaR - R library","pathname":"/develop-2/manual/using-opencga/client-libraries/r","siteSpaceId":"sitesp_rfm3A","description":"If you're a R user and you're keen of running OpenCGA through R, you're in the right place!","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MQ4hWj27UEVi787TdkU","title":"Java","pathname":"/develop-2/manual/using-opencga/client-libraries/java","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MQ4hWj5AVDQ_I01740c","title":"JavaScript","pathname":"/develop-2/manual/using-opencga/client-libraries/javascript","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MQ4hWj6q7iZkn6wxuRQ","title":"Command Line","pathname":"/develop-2/manual/using-opencga/command-line","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MgMK83BJiXB5XoPyddY","title":"Configuration","pathname":"/develop-2/manual/using-opencga/command-line/configuration","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Command Line"}]},{"id":"-MbfHY6QvRj4zWwYI_cm","title":"Files","pathname":"/develop-2/manual/using-opencga/command-line/files","siteSpaceId":"sitesp_rfm3A","description":"opencga.sh files","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Command Line"}]},{"id":"-MQ4hWj7nl9oanljn4ys","title":"Public Demo","pathname":"/develop-2/manual/using-opencga/public-demo","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MQ4hWjE5wYMkjP_AQgu","title":"Managing Data","pathname":"/develop-2/manual/data-management","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MlPjWbAKhPp0GwJAaZd","title":"Working with Projects and Studies","pathname":"/develop-2/manual/data-management/projects-and-studies","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MlPg7Yd18oNGVQxY41u","title":"Loading of VCF files","pathname":"/develop-2/manual/data-management/ingestion-of-vcf-files","siteSpaceId":"sitesp_rfm3A","description":"This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store.","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MQ4hWjGAlB_vUxzN3ZK","title":"Working with Files","pathname":"/develop-2/manual/data-management/working-with-files","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MiWZPU7YiUZDG3ekgi-","title":"Sharing and Permissions","pathname":"/develop-2/manual/data-management/sharing-and-permissions","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MkqVwVW5DJAHCkMUxJH","title":"Users and Groups","pathname":"/develop-2/manual/data-management/sharing-and-permissions/users-and-groups","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Sharing and Permissions"}]},{"id":"-MiWZPU8aW2jlxH5Klwx","title":"Study ACLs","pathname":"/develop-2/manual/data-management/sharing-and-permissions/permissions","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Sharing and Permissions"}]},{"id":"-MlEUDomZ2wkbu6pJYCS","title":"Population of metadata","pathname":"/develop-2/manual/data-management/population-of-metadata","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MiWZPU9aGvX4HPlekwE","title":"Data Versioning","pathname":"/develop-2/manual/data-management/population-of-metadata/data-versioning","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Population of metadata"}]},{"id":"-MiWZPUAKbgbvRwmtIRe","title":"Adding Custom Metadata","pathname":"/develop-2/manual/data-management/population-of-metadata/adding-custom-metadata","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Population of metadata"}]},{"id":"-MQ4hWjJbho2nmEGMCF1","title":"Alignment Engine","pathname":"/develop-2/manual/alignment-engine","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MQ4hWjKPo3HYix4M6Sr","title":"BAM Index","pathname":"/develop-2/manual/alignment-engine/bam-index","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MQ4hWjL1-qlbV5QExtM","title":"Alignment Read Query","pathname":"/develop-2/manual/alignment-engine/alignment-read-query","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MQ4hWjMZx8JNm8qSe3U","title":"Working with Coverage","pathname":"/develop-2/manual/alignment-engine/working-with-coverage","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MQ4hWjNhkCQb_lI0Pn5","title":"Alignment Analysis","pathname":"/develop-2/manual/alignment-engine/alignment-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MQ4hWjOaKqfBmnyMLqN","title":"Variant Storage Engine","pathname":"/develop-2/manual/variant-storage-engine","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MQ4hWjQYZWXaPz9Wg1t","title":"Variant Query","pathname":"/develop-2/manual/variant-storage-engine/variant-query","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MQ4hWjR5BD4KRHI4TS9","title":"Variant Aggregation Stats","pathname":"/develop-2/manual/variant-storage-engine/variant-aggregation-stats","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MQ4hWjSfeAaiMdB6CrO","title":"Variant Analysis","pathname":"/develop-2/manual/variant-storage-engine/variant-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MQ4hWjTIPULeq-nu9Dj","title":"Clinical Genomics","pathname":"/develop-2/manual/clinical-genomics","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDuu8KTY5bfdvNIitA","title":"Clinical Interpretation","pathname":"/develop-2/manual/clinical-genomics/clinical-interpretation","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Clinical Genomics"}]},{"id":"-MQ4hWinrw4Sqtrzgj7q","title":"Clinical Analysis","pathname":"/develop-2/manual/clinical-genomics/clinical-analysis","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Clinical Genomics"}]},{"id":"-MQ4hWjWnGE7iXmAG2m7","title":"Using JupyterLab","pathname":"/develop-2/manual/using-jupyterlab","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MQ4hWjXcSWVqD3pgEot","title":"Administrator","pathname":"/develop-2/manual/administrator","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MQ4hWjY33mdVovFxkiy","title":"User Management","pathname":"/develop-2/manual/administrator/user-management","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Administrator"}]},{"id":"-MZSY1mVF1Hpip5HLWGF","title":"Templates / Manifest","pathname":"/develop-2/manual/administrator/templates-manifest","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Administrator"}]},{"id":"-MHDweppWqP-H1nFjtaT","title":"Roadmap","pathname":"/develop-2/about/roadmap","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"About"}]},{"id":"-MHDtSkKkNddzPI0ZQ3A","title":"Release Notes","pathname":"/develop-2/about/release-notes","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"About"}]},{"id":"-MHJCORLnz3Y7VmwKBrS","title":"Community","pathname":"/develop-2/about/contributing","siteSpaceId":"sitesp_rfm3A","description":"","breadcrumbs":[{"label":"About"}]},{"id":"-MHDrXvrawJl4gZ11rNo","title":"Home","pathname":"/","siteSpaceId":"sitesp_ZwsL0","description":"Welcome to the official page for OpenCGA documentation."},{"id":"-MHECj6Xj1FnH4Ewr2lf","title":"Overview","pathname":"/overview","siteSpaceId":"sitesp_ZwsL0","description":""},{"id":"-MNGRj82nxY7Ucn2Udfs","title":"Features","pathname":"/overview/features","siteSpaceId":"sitesp_ZwsL0","description":"Overview of main features","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGTXRwXhCL3-IuQTQq","title":"Architecture Diagram","pathname":"/overview/architecture","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGUUShDqvDF59XwhZ-","title":"Security","pathname":"/overview/security","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGUYX4-_U6ZBBF8Npp","title":"Metadata and Clinical Data","pathname":"/overview/data-management","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNLmmzromP_oErear5-","title":"Data Models","pathname":"/overview/data-models","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNLMBLCBXxob_znoEDn","title":"Sample","pathname":"/overview/data-models/sample","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"},{"label":"Data Models"}]},{"id":"-MNQQ8IENJcYoXxMVT-o","title":"Individual","pathname":"/overview/data-models/individual","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"},{"label":"Data Models"}]},{"id":"-MNLQSJc6Njsuls0Qp1k","title":"Alignment and Coverage","pathname":"/overview/alignment-and-coverage","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGUi_2Pn6jQzmN-LkS","title":"Variant Query and Analysis","pathname":"/overview/variant-query-and-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGUo_xQN921Ly4NBWh","title":"Clinical Data Analysis","pathname":"/overview/clinical-data-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGUxvKIjbsu5nB8ryy","title":"Running Analysis","pathname":"/overview/running-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGVaDS0FJ0nNvoHNa-","title":"Scalability and Performance","pathname":"/overview/scalability-and-performance","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNGV5WR8Eb8UtYxBMat","title":"Sizing OpenCGA","pathname":"/overview/sizing-opencga","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Overview"}]},{"id":"-MNLIM6ClAwek5P5I6Ez","title":"OpenCGA Architecture","pathname":"/components-1","siteSpaceId":"sitesp_ZwsL0","description":""},{"id":"-MHDuXgVi2FhepgQloAv","title":"Catalog","pathname":"/components-1/catalog","siteSpaceId":"sitesp_ZwsL0","description":"Metadata and Clinical Data Database","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDwqxCbxOY-lD7i5Uo","title":"Alignment and Coverage","pathname":"/components-1/alignment-and-coverage","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDuare_SumKP8IACv3","title":"Variant Storage Engine","pathname":"/components-1/variant-storage","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDuu8KTY5bfdvNIitA","title":"Clinical Analysis","pathname":"/components-1/clinical","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MHDwNNkV4gGTqUn9fbx","title":"Analysis Framework","pathname":"/components-1/analysis-framework","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"OpenCGA Architecture"}]},{"id":"-MfLlfVB5g14vX69XoU0","title":"Data Models","pathname":"/data-models","siteSpaceId":"sitesp_ZwsL0","description":""},{"id":"-MfV0R2FwHt8UEG-vTkk","title":"User","pathname":"/data-models/user","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2GURwC8t9GWa3H","title":"Project","pathname":"/data-models/project","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2HJIkJekbGwyJq","title":"Study","pathname":"/data-models/study","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2IqyvTDpR8w2e6","title":"File","pathname":"/data-models/file","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfLlfVC7oP5NEPOizk0","title":"Sample","pathname":"/data-models/sample","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfLlfVDzLwb6JVIm5Nq","title":"Individual","pathname":"/data-models/individual","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2LNPf_Hr1Yt-Ws","title":"Family","pathname":"/data-models/family","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2ML2mexIkVd1BU","title":"Cohort","pathname":"/data-models/cohort","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MfV0R2Nf9vINfhkT8Iw","title":"Job","pathname":"/data-models/job","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MlU0BvXKDNUkKmoyna3","title":"Clinical Analysis","pathname":"/data-models/clinical-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Data Models"}]},{"id":"-MHDxqjggzacPuAiMMi7","title":"Case Studies","pathname":"/case-studies","siteSpaceId":"sitesp_ZwsL0","description":""},{"id":"-MHDxx8km4oR423iZ_so","title":"Genomics England Research","pathname":"/case-studies/genomics-england-research","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"Case Studies"}]},{"id":"-MHDy5GJaAwAd3o2X47D","title":"Microsoft Azure","pathname":"/case-studies/microsoft-azure","siteSpaceId":"sitesp_ZwsL0","description":"Azure HDInisght","breadcrumbs":[{"label":"Case Studies"}]},{"id":"-MHDtC51-Gdzm_1m6XtR","title":"Installation","pathname":"/manual/installation","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDrtMRS4G4Z5Esr1Mz","title":"Kubernetes Cluster","pathname":"/manual/installation/kubernetes","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MHDsBAq2SOy8Vls3UyS","title":"Azure","pathname":"/manual/installation/kubernetes/azure","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"Kubernetes Cluster"}]},{"id":"-MI1j74ncPkSxHUKrPG8","title":"Configuration","pathname":"/manual/installation/kubernetes/configuration","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"Kubernetes Cluster"}]},{"id":"-MHDryfAb6qrpYJfb19y","title":"On-Premise HPC Cluster","pathname":"/manual/installation/compute-cluster","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MHDsG2-eQLC3RiStR5S","title":"Server Configuration","pathname":"/manual/installation/compute-cluster/server-configuration","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MI1jJW1KbCJXdeLkuzC","title":"Getting OpenCGA","pathname":"/manual/installation/compute-cluster/building-from-source","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MI1jRcPxhKBkE5tN_ka","title":"Choosing Variant Storage Engine","pathname":"/manual/installation/compute-cluster/chosing-variant-storage","siteSpaceId":"sitesp_ZwsL0","description":"HBase vs. MongoDB","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MNBrgGRLxOyHtbeNtVs","title":"Configuration","pathname":"/manual/installation/compute-cluster/configuration","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"},{"label":"On-Premise HPC Cluster"}]},{"id":"-MHDrhJgw20RM4PEKcIM","title":"Running Docker","pathname":"/manual/installation/docker","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Installation"}]},{"id":"-MNLIerBARfz3ku9KZiY","title":"Login","pathname":"/manual/login","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDtwi8Qn-RqZ1VfF9-","title":"Using OpenCGA","pathname":"/manual/using-opencga","siteSpaceId":"sitesp_ZwsL0","description":"You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started!","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MHDuPyYw1eYfH7fKQLM","title":"REST Web Service API","pathname":"/manual/using-opencga/restful-web-service-api","siteSpaceId":"sitesp_ZwsL0","description":"Understanding REST web service API","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MNHJDXYbJcY343J38OW","title":"IVA Web App","pathname":"/manual/using-opencga/iva-web-app","siteSpaceId":"sitesp_ZwsL0","description":"A rich web app front-end to work with OpenCGA","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MNHH0YNRfT4fdBeXJgH","title":"Client Libraries","pathname":"/manual/using-opencga/client-libraries","siteSpaceId":"sitesp_ZwsL0","description":"Java, Python, R and Javascript clients are implemented","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MNHHQAFe-vPx5l2OuPx","title":"pyopencga - Python Library","pathname":"/manual/using-opencga/client-libraries/python","siteSpaceId":"sitesp_ZwsL0","description":"If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place!","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MNHHVCF1VmGR4m4_p55","title":"opencgaR - R library","pathname":"/manual/using-opencga/client-libraries/r","siteSpaceId":"sitesp_ZwsL0","description":"If you're a R user and you're keen of running OpenCGA through R, you're in the right place!","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MNHHM6-X29YPOFoOZIH","title":"Java","pathname":"/manual/using-opencga/client-libraries/java","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MNHHXEBiicSCkJkNuE9","title":"JavaScript","pathname":"/manual/using-opencga/client-libraries/javascript","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Client Libraries"}]},{"id":"-MNHJ4g9eyS_0kXGGRJf","title":"Command Line","pathname":"/manual/using-opencga/command-line","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MgMKTeWWBw4mNCjpZgp","title":"Configuration","pathname":"/manual/using-opencga/command-line/configuration","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"},{"label":"Command Line"}]},{"id":"-MNHBe0ySHxYYAk5M9XC","title":"Public Demo","pathname":"/manual/using-opencga/public-demo","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Using OpenCGA"}]},{"id":"-MNLIpb2vvTHdf2zyiVl","title":"Managing Data","pathname":"/manual/data-management","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLJO0vhtb4Dt16k3fa","title":"Sharing and Permissions","pathname":"/manual/data-management/sharing-and-permissions","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MjdVdOpOp6J95OqWHdl","title":"Users and Groups","pathname":"/manual/data-management/sharing-and-permissions/users-and-groups","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Sharing and Permissions"}]},{"id":"-MhU7akSONP6xJJyRhMv","title":"Study ACLs","pathname":"/manual/data-management/sharing-and-permissions/permissions","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Sharing and Permissions"}]},{"id":"-MNLJ3WoCKn0UpBhnLOZ","title":"Create Projects and Studies","pathname":"/manual/data-management/projects-and-studies","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MNLJfwqAJNVsKiAJcEz","title":"Load VCF Files to a Study","pathname":"/manual/data-management/ingestion-of-vcf-files","siteSpaceId":"sitesp_ZwsL0","description":"This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store.","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MNLJAVRAei-1VEpkbZL","title":"Working with Files","pathname":"/manual/data-management/working-with-files","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-Mkvt9JsSovdhyqsH_9b","title":"Population of Metadata","pathname":"/manual/data-management/population-of-metadata","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"}]},{"id":"-MNLJImVurAQxVvuu0Jw","title":"Adding Custom Metadata","pathname":"/manual/data-management/population-of-metadata/adding-custom-metadata","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Population of Metadata"}]},{"id":"-MgAgrU8lp5f4FE77IGv","title":"Data Versioning","pathname":"/manual/data-management/population-of-metadata/data-versioning","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Managing Data"},{"label":"Population of Metadata"}]},{"id":"-MNLKSfNmfK62x9PP1VY","title":"Alignment Engine","pathname":"/manual/alignment-engine","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLL5X-3WHr0Kszv9j_","title":"BAM Index","pathname":"/manual/alignment-engine/bam-index","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MNLL0jEZNrZdBEaUNHt","title":"Alignment Read Query","pathname":"/manual/alignment-engine/alignment-read-query","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MNLKywfNikV6ex-moAq","title":"Working with Coverage","pathname":"/manual/alignment-engine/working-with-coverage","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MNLKuj1klp2c2H1bOKv","title":"Alignment Analysis","pathname":"/manual/alignment-engine/alignment-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Alignment Engine"}]},{"id":"-MNLJWAscB6UTjs9TWkn","title":"Variant Storage Engine","pathname":"/manual/variant-storage-engine","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLJkqneInAIU5wjwE4","title":"Variant Query","pathname":"/manual/variant-storage-engine/variant-query","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MNLJpFg40yH6SY02DqQ","title":"Variant Aggregation Stats","pathname":"/manual/variant-storage-engine/variant-aggregation-stats","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MNLK-NKxnWuT6kWCSvI","title":"Variant Analysis","pathname":"/manual/variant-storage-engine/variant-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Variant Storage Engine"}]},{"id":"-MNLKEJa25P9yyCSb3iF","title":"Clinical Genomics","pathname":"/manual/clinical-genomics","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLKhVxXMv2mdSJTvB5","title":"Clinical Interpretation","pathname":"/manual/clinical-genomics/clinical-interpretation","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Clinical Genomics"}]},{"id":"-MlU0BulGad3W7RR50VH","title":"Clinical Analysis","pathname":"/manual/clinical-genomics/clinical-analysis","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Clinical Genomics"}]},{"id":"-MNLx_MDLcZGt9V2oebA","title":"Using JupyterLab","pathname":"/manual/using-jupyterlab","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLKGy7HBEI9H3bLJ3R","title":"Administrator","pathname":"/manual/administrator","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"}]},{"id":"-MNLKmppEoOEIYsXBNcO","title":"User Management","pathname":"/manual/administrator/user-management","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Administrator"}]},{"id":"-MgMN4UzGlU6K_958wRM","title":"Templates / Manifest","pathname":"/manual/administrator/templates-manifest","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"User Manual"},{"label":"Administrator"}]},{"id":"-MHDweppWqP-H1nFjtaT","title":"Roadmap","pathname":"/about/roadmap","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"About"}]},{"id":"-MHDtSkKkNddzPI0ZQ3A","title":"Release Notes","pathname":"/about/release-notes","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"About"}]},{"id":"-MHJCORLnz3Y7VmwKBrS","title":"Community","pathname":"/about/contributing","siteSpaceId":"sitesp_ZwsL0","description":"","breadcrumbs":[{"label":"About"}]}]}