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OpenCGA is still under a very active development, we are heading to the first stable release in 2017 Q2, you can find more detailed information in GitHub Releases at

1.3.0 (November 2017)


  • [FEATURE] Admin migration command line (#690)


  • [REMOVE] Remove ACL from data models. (#666)
  • [ENHANCEMENT] Clean old code and refactoring. (#667, #668, #669, #670)
  • [ENHANCEMENT] Remove some hidden and deprecated methods from webservices and command line (#672)
  • [CHANGE] Changes to family data model (#677)
  • [FEATURE] Add new analysis tool webservices (#679)
  • [FEATURE] Add version support for SampleIndividual and Family (#684)
  • [ENHANCEMENT] Clean and remove unnecessary dependencies for the client module (#687)
  • [ENHANCEMENT] Change some fields from Clinical Analysis (BETA) data model (#688, #702)
  • [ENHANCEMENT] Remove unnecessary Relatives data model (#693)
  • [ENHANCEMENT] Improve some individual webservices to better support the Individual-Sample relation (#701)
  • [CHANGE] Change individual parameter in the sample/create webservice (#703)
  • [CHANGE] Internal modification regarding the way the Sample-Individual relation was stored (#706)
  • [ENHANCEMENT] Add new admins group in studies (#711)
  • [ENHANCEMENT] Add new stats field to Sample data model (#717)
  • [CHANGE] Rename ontologyTerms field in Sample, Individual and diseases field in Family for phenotypes (#718)
  • [FEATURE] Add new option to export and import data from/to catalog (#720)
  • [ENHANCEMENT] Improve groupby webservices (#721)
  • [ENHANCEMENT] Support a list of ids in all GET webservices (#727)
  • [CHANGE] Internal modification: Change ACL delimiter used (#740)

Variant Storage

  • [FEATURE] Make use of the new VariantMetadata model from Biodata (#673)
  • [FEATURE] Major support of Symbolic variants in Variants Storage (#695)
  • [FEATURE] Create profiles to select hadoop flavour (s#707)
  • [FEATURE] Store info fields on storage-hadoop improvement storage (#704)
  • [FEATURE] Allow loading multiple variant files from the same sample with non overlapping variants (#696)
  • [FEATURE] New optional pipeline step "fill-gaps" (#713)
  • [CHANGE] Rename some Variant REST query parameters (#751)
  • [CHANGE] GO and EXPRESSION filter must be combined as an AND with other region (#694)
  • [CHANGE] Update CellBase to v4.5.3 improvement (#770)
  • [ENHANCEMENT] Speed up GENOTYPE filter with FILES filter, when possible (#675)
  • [ENHANCEMENT] Add field "source" to VariantQueryResult (#758)
  • [ENHANCEMENT] Indicate if "numTotalResults" is an approximated count in VariantQueryResult (#749)
  • [FIX] Inconsistent configuration param to select variant annotator (#747)
  • [FIX] Duplicate Key Warn/Error in Stage Collection (#766)
  • [FIX] IllegalArgumentException when CellBaseRestVariantAnnotator skips a variant (#746)
  • [FIX] Concurrent table modification error when loading in Hadoop with merge=basic (#709)

1.2.0 (September 2017)


  • [FIX] Fix job search by input and output files. (#533)
  • [ENHANCEMENT] Hide deprecated webservices. (#599)
  • [ENHANCEMENT] Set ontologyTerms array during Sample/Individual /create and /update webservices. (#613)
  • [FEATURE] Add the concept of release in OpenCGA. (#616)
  • [FIX] Fix behaviour where individual ids are not recognized when creating new family. (#617)
  • [FEATURE] Implement JWT based session management (#618)
  • [ENHANCEMENT] Change List<Long> for List<Object> in corresponding data models (#621)
  • [ENHANCEMENT] Make ACL permissions part of the query (#628)
  • [FIX] Fix count parameter not working in search webservices and command line (#629)
  • [CHANGE] Change annotationsets REST webservices. (#631)
  • [FEATURE] Support multigroups (#633)
  • [ENHANCEMENT] Return HTTP 403 error code when user tries to access not granted data (#636)
  • [FEATURE] Add a new members group for every study (#642)
  • [FEATURE] Automatically sync OpenCGA groups with external LDAP groups during login (#647)
  • [FEATURE] Add new projects/search webservice (#651)
  • [FEATURE] Add new confidential parameter to VariableSet data model. It allows defining confidential variable sets and corresponding annotation sets, so a new special permission will be needed to access them. (#653)
  • [FEATURE] Propagate permissions from samples to individuals. (#657)
  • [ENHANCEMENT] Return HTTP 401 error code when user is not successfully logged in or the token is invalid. (#658)

Variant Storage

  • [FEATURE] Improve Solr integration with VariantStorage when querying (#638)
  • [ENHANCEMENT] Improve Solr variant iterator by using Solr cursors (#640)
  • [ENHANCEMENT] Variant Solr Search manager improvements (#639)
  • [ENHANCEMENT] Configure VariantMerger and VariantNormalizer with VCFHeader (#630)
  • [ENHANCEMENT] Store DisplayConsequenceType from VariantAnnotation at MongoDB (#659)
  • [ENHANCEMENT] Return VariantTraitAssociation as TraitAssociation (EvidenceEntry) (#692)
  • [FEATURE] Remove files from variants storage (#192)
  • [FEATURE] Command line and rest endpoints for remove operations on variant storage (#623)
  • [FEATURE] Simple merge mode for loading variants in opencga-storage-hadoop (#609)
  • [FEATURE] VariantQueryParam INCLUDE_FORMATS. Select format fields to return (#608)
  • [FEATURE] Store other genotype fields on storage-hadoop (#602)
  • [FEATURE] Export variant statistics (#309)
  • [FIX] Sample filter not working when the sample is in multiple files (#641)
  • [FIX] Possible error loading overlaping multiallelic variants (#626)
  • [FIX] Do not delete files (or related entries) from catalog if still loaded in variants storage (#625)
  • [FIX] Avoid OutOfMemoryError updating storage metadata from catalog (#645)
  • [FIX] Error indexing vcf files containing "variants" in the file name(#691)
  • ----- PENDING [ENHANCEMENT] Add more Variant permissions to Study and Sample (#481)

Relevant changes 

1.1.0 (June 2017)


  • [ENHANCEMENT] Support integers and floats type for variables. (#545)
  • [BUG] Fix link race condition. (#551)
  • [FEATURE] Add new parameter propagate to Individual web service when setting permissions to propagate permissions to the related samples. (#558)
  • [FEATURE] Add support to give permissions using queries in sample, individual and file web services. (#560)
  • [CHANGE] Change Acl REST web services. (#561)
  • [FIX] Not return fields that are of no interest (using include/exclude). (#569)
  • [FEATURE] Add new admin command line to synchronise and add users from LDAP groups. (#573)
  • [FEATURE] Added new Family data model. (#582)
  • [FEATURE] Add list<Sample> to individual/create web service. (#583)
  • [FEATURE] Add new /meta/status, /meta/ping and /meta/about web services. (#572)
  • [ENHANCEMENT] Support creating an Individual when calling to the Sample create web service. (#586)
  • [DEPRECATE] Deprecate species field of Individual data model. (#588)
  • [ENHANCEMENT] Deprecate usage of variableSetId. Add field variableSet to corresponding web services that accepts an id or a name. (#589)
  • [ENHANCEMENT] Support passing an array of annotationSets when creating an Annotable entry (Sample, Cohort, Individual and Family). (#590)
  • [ENHANCEMENT] Add new type field to Sample model. (#591)
  • [FEATURE] Add father and mother information in attributes field of Individual. (#592)
  • [ENHANCEMENT] Add support to change public/private User registration  (#594)
  • [DEPRECATE] Deprecate all xx/create and xx/update GET webservices. (#598)

Variant Storage

  • [FEATURE] Make optional to merge non same overlapping variants in MongoDB (#574)
  • [FEATURE] Implement a benchmark framework for OpenCGA Storage (#248)
  • [ENHANCEMENT] Filter VcfRecord before converting into Variant object when possible (#577)
  • [BUGFIX] Not loading new overlapping variants in HBase (#581)
  • [ENHANCEMENT] Increment variant size threshold for CellBase annotation (#596)
  • [BUGFIX] Fix ArrayIndexOutOfBounds when loading variants data (#597)
  • [FEATURE] Add VCF export to gRPC command line (#606)

Relevant changes - migration

  • Add new permissions to admin user in the general configuration file. To add: VIEW_STUDY, UPDATE_STUDY and SHARE_STUDY
  • Added sampleIds parameter in each individual entry. 
  • Catalog changes require this migration script: opencga-1.1.0-migration.js
  • Changes of #574 require to execute a migration script on all Variants databases in MongoDB: opencga_574_add_studies_field_to_stage.js



  • [BUGFIX] Fix VCF output format (#584)


  • [ENHANCEMENT] New dateOfBirth field added to Individual (#580) and somatic field to Sample (#576)
  • [ENHANCEMENT] Performance improvement when annotating new variants (#575)

1.0.0 (February 2017)


  • [FIX] Authenticated users can now see public data (#501)
  • Permissions assigned to individuals are directly propagated to samples (#509)
  • [CHANGED] CREATE and UPDATE permissions have been merged into WRITE (#506)
  • [CHANGED] Permissions given to folders are now propagated in the database (#505), this increase significantly the performance of the ACL resolution 
  • [CHANGED] Changes in session data model (#479)


  • Complete the implementation of exclude and include of fields for Variant queries (#515)


  • [Python] new Python client implemented following the same architecture than Java and Javascript clients ( This improves the quality significantly and add many new features, thanks Antonio Rueda!
  • Java and Javascript client libs use always POST when available


  • [REST] Add new files/create using POST to create new folders and files with some content (#514)
  • [REST] Rename parameters from acl/update (2617993)
  • [REST] Hide from Swagger all create and update ACL web services using GET (cbea817), these should always use POST, this affects to studies, samples, files, ... (these will be removed in version 1.1) 
  • [REST] Complete the implementation of exclude and include of fields for Variant queries
  • [REST] Remove from users the GET methods to create and update filters (5125a22)
  • [REST] Add a warning to Swagger to all create and update methods using GET (ee6d66). It is encourage that all create and update actions use always POST
  • [GRPC] Complete the implementation of exclude and include of fields for Variant queries

1.0.0-rc3 (January 2017)


  • Major changes in maven properties and configuration files. (#480)
  • catalog-configuration.yml and configuration.yml have been merged. (#476)


  • Added support to fetch shared projects and studies.
  • Added organism information to the project data model. (#455)
  • Renamed diskUsage and diskQuota for size and quota respectively in all data models were present.
  • Closed sessions are now removed from the array of sessions (but they can still be found in the audit collection). (#475)


  • Improve error handling for storage operations (#447#463#465)
  • Add param --resume to and command line (#465)
  • Import and export variants datasets (#459#460)
  • Enable gRPC as top level feature (#492)
  • New top layer StorageManager connecting catalog with storage (#486)
  • Shade proto and guava dependencies for Hadoop (#440)


  • Create and update webservices have been all implemented via POST.

Known issues

  • OpenCGA storage hadoop is not available in this version. To compile use this line:

    mvn clean install -DskipTests -pl '!:opencga-storage-hadoop-core'

1.0.0-rc2 (November 2016)

1.0.0-rc1 (September 2016)

This release constitutes the first release candidate (RC1). This is the biggest release ever with more than 1,400 commits, special mention to j-coll and pfurio for their contribution in Catalog, Storage and Server components.


  • New command line interfaces (CLI) for users (, admins ( and analysis (


  • New catalog configuration file using YAML.
  • New authorisation method. A big list of permission have been defined.
  • New smart id resolver. Numerical ids are no longer mandatory and ids are now resolved internally given the alias.
  • New and improved java and python command lines.
  • New javascript, java and R client implementations.
  • Support for annotations in cohorts.


  • Many performance improvements and fixes in MongoBD storage engine, the most notable include a new load strategy to improve file merging scalability
  • New storage engine based on Apache HBase, this is completely functional but is tagged as beta until more tests are done.
  • New custom variant annotation implemented


  • An experimental gRPC server implemented


Third Beta


Second Beta


First Beta

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