The GA4GH server is currently under active development, and several features are not yet fully functional. These mostly involve the reads API. Some missing features are:

  • Unmapped reads. We do not support searching for unmapped reads.
  • Searching over multiple ReadGroups in different ReadGroupSets.

For more detail on individual development issues, please see the project’s issue page.

Release Notes


This an alpha pre-release that contains some major updates. The most important changes are highlighted in bold below. We have also made some updates to the documentation.


  • Rename package from “ga4gh” to “ga4gh-server” #1582, #1583
  • Added support for BigWig files in a new Continuous Data object #1573 New endpoints and message types include:
  • POST /continuoussets/search
  • GET /continuoussets/{id}
  • POST /continuous/search
  • Continuous (new)
  • ContinuousSet (new)
  • Add ability to list and join peer server networks #1507 New endpoints and message types include:
  • POST /peers/list
  • POST /peers/announce
  • GET /info
  • ListPeersResponse (new)
  • Peer (new)
  • AnnouncePeerResponse (new)
  • GetInfoResponse (new)
  • Remove feature_id from ExpressionLevel and add ability to search by the Name field #1580 Impacts
  • POST /expressionlevels/search
  • GET /expressionlevels/{id}
  • Replaced info fields with rich type Attributes fields #1521 Impacts the following message types:
  • TranscriptEffect
  • VariantAnnotation
  • Individual
  • Biosample
  • Experiment (new)
  • Analysis (new)
  • Dataset
  • ReadGroup
  • ReadGroupSet
  • ReadAlignment
  • Reference
  • ReferenceSet
  • RnaQuantificationSet
  • RnaQuantification
  • ExpressionLevel
  • Feature
  • VariantSetMetadata
  • CallSet
  • Call
  • Variant
  • Replace NCBI taxon ID integer with ontology term #1551 Impacts the following message types:
  • Reference
  • ReferenceSet
  • Changed ontology term “id” to “term_id” #1513 Impacts the following message types:
  • OntologyTerm


  • Document auto-releases, constraint instructions #1578
  • Improved development document for virtualenv command #1550


  • Automatically deploy tagged releases to Pypi from Travis #1576
  • Refactor transcript annotation #1334
  • Speedups to rna quantification ingest #1564


Alpha pre-release supporting minor update. We have done some restructuring, some bug fixes and some minor protocol updates in this release.

  • Restructuring: We have reorganized our codebase to separate out the schemas,
    client, and server components as separately installable Python components. Running ‘pip install ga4gh –pre’ will still automatically install all required packages. But now developers who wish to leverage the Python libraries around the schemas can just use ‘pip install ga4gh-schemas’, and developers of client code can gain access to the client API library my just running ‘pip install ga4gh-client’.
  • Bug fixes and improvements
    • Fix to be able to handle VCFs with genotype == ‘./.’ (server #1389)
    • Fixed bug with OIDC Authentication (server #1452, #1508)
    • Repo manager list out of range error (server #1472)
    • G2P features search was returning a 404, this has been fixed (server #1379)
    • Sped up readGroupSet generator (server #1316)
    • Enhanced ENCODE RNA downloader
    • Added support for Auth0 (server #1452)
    • Refactored usage of the term ‘biosample’ to be consistent (server #1394)
    • Moved to Protobuf version 3.1 (server #1471)
  • Documentation updates
    • Github usage
    • Added sections for new Python packages: client and schemas
    • Split out repository manager docs
    • Docker file documentation updated
    • Updated the Configuration section to document the Auth0 settings


Alpha pre-release supporting major feature update.

  • G2P functionality added to support the following API endpoints:
    • POST /phenotypeassociationsets/search
    • POST /phenotypes/search
    • POST /featurephenotypeassociations/search
  • Biometadata tags for RNA quantifications.
  • Improvements to the RNA quantification ingestion pipeline.
  • Migrated CLI related code to cli module.
  • Add demonstration RNA quantification data.
  • Minor doc fixes

Known Issues

  • When searching using a wildcard, *, an Internal Server Error occurs. #1379
  • When listing many Read Group Sets, responses can be quite slow causing timeouts. #1316


Alpha pre-release supporting major feature update.

  • RNA functionality added to support the following API endpoints:
    • POST /rnaquantificationsets/search
    • GET /rnaquantificationsets/{id}
    • POST /rnaquantifications/search
    • GET /rnaquantifications/{id}
    • POST /expressionlevels/search
    • GET /expressionlevels/{id}
  • Fixed bug where transcript effects would be repeated within a search result.


Alpha pre-release supporting major feature update.

  • Metadata functionality added to support biosample and individual metadata capabilities.
  • Now support searching features by ‘name’ and ‘gene_symbol’. These fields have been promoted to facilitate the future integration of the RNA and G2P modules.


Alpha pre-release supporting major feature update. This release is not backwards compatible with previous releases due to several changes to the schemas that were required to move to protocol buffers.

  • This release includes the code changes necessary for the migration to protocol buffers from Avro.
  • Client applications will need to be rebuilt to the new schemas and use the protobuf json serialization libraries to be compatible with this version of the server.


Alpha pre-release supporting major feature update. This release is not backwards compatible with previous releases, and requires the data files be re-imported.

  • File locations are now tracked in a registry.db registry such that the files can be located anywhere. The information from the json sidecar files are also included in the database.
  • Ontology terms are now imported via an OBO file instead of the old pre-packaged sequence_ontology.txt file. A sample OBO file has been added to the sample data set for the reference server.
  • Added a custom landing page option for the main page of the server.
  • Performance improvement for variant search when calls are set to an empty string.
  • Improved server configuration including Apache configuration and robots.txt file.


Alpha pre-release supporting major feature update. This release is backwards incompatible with previous releases, and requires a revised data directory layout.

  • Added sequence and variant annotations (which introduces a sqlite database component)
  • Added repo manager, a command line tool to manage data files and import them into the server’s data repository
  • Supported searching over multiple ReadGroups, so long as they are all in the same ReadGroupSet and all of the ReadGroups in the ReadGroupSet are specified


Bugfix release that fixes a problem introduced by upstream package changes


Alpha pre-release supporting major schema update. This release is backwards incompatible with previous releases, and requires a revised data directory layout.

  • Schema version changed from v0.5 to v0.6.0a1
  • Various backwards incompatible changes to the data directory layout
  • Almost complete support for the API.
  • Numerous code layout changes.


This bugfix release addresses the following issues:

  • #455: bugs in reads/search call (pysam calls not sanitized, wrong number of arguments to getReadAlignments)
  • #433: bugs in paging code for reads and variants


  • Fixes dense variants not being correctly handled by the server (#391)
  • Removes unused paths (thus they won’t confusingly show up in the HTML display at / )


Just bumping the version number to 0.1.0.


This is a beta pre-release of the GA4GH reference implementation. It includes

  • A fully functional client API;
  • A set of client side tools for interacting with any conformant server;
  • A partial implementation of the server API, providing supports for variants and reads from native file formats.


This is an early alpha release to allow us to test the PyPI package and the README. This is not intended for general use.