ga4gh-schemas v1.0.1

.. figure:: http://genomicsandhealth.org/files/logo_ga.png :alt: Image

Schemas for the Data Working Group !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

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The Global Alliance for Genomics and Health <http://genomicsandhealth.org/>__ is an international coalition, formed to enable the sharing of genomic and clinical data.

The Data Working Group <http://genomicsandhealth.org/working-groups/data-working-group>__ concentrates on data representation, storage, and analysis, including working with platform development partners and industry leaders to develop standards that will facilitate interoperability.

Each area of genomics and health has a dedicated team working to define those standards.

Reads Task Team @@@@@@@@@@@@@@@

The Reads Task Team <https://groups.google.com/forum/#!forum/dwgreadtaskteam>__ is focused on standards for accessing genomic read data -- collections of primary data collected from sequencing machines.

The team will deliver:

#. Data model. An abstract, mathematically complete and precise model of the data that is manipulated by the API. See the Proto directory <src/main/proto>__ for our in-progress work on defining v0.5 of the data model.

#. API Specification. A human-readable document introducing and defining the API, accompanied by a formal specification. See the documentation page <http://ga4gh.org/#/apis/reads/v0.1>__ for the published v0.1 API.

#. Reference Implementation. Open source working code demonstrating the API, ideally which can underpin real world working implementations.

Reference Variation Task Team @@@@@@@@@@@@@@@@@@@@@@@@@@@@@

The Reference Variation Task Team is focused on standards for storing and accessing reference genome and variant data -- the results of analysis of primary data collected from sequencing machines.

Variant Annotation Task Team @@@@@@@@@@@@@@@@@@@@@@@@@@@@@

The Variant Annotation Task Team is focused on developing standards for reporting variant annotation including results formats, ontologies and vocabularies for different classes of annotation so reporting is consistent and in a manner that facilitates benchmarking and evaluation.

File Formats Task Team @@@@@@@@@@@@@@@@@@@@@@

One small but essential part of this effort is the definition, standardisation, and improvement of basic file formats for sequence and variation data, and for associated infrastructure such as index formats.

These format specifications can be found in the samtools/hts-specs repository <https://github.com/samtools/hts-specs>__.

Metadata Task Team @@@@@@@@@@@@@@@@@@

The Metadata Task Team (MTT) concerns itself with data structures, attributes and values used to describe everything but the sequence. This includes metadata for individuals, samples, analyses, instrumentation a well as ontology representations for metadata. Naturally, the group interacts heavily with members of most other task teams and working groups.

MTT Wiki <https://github.com/ga4gh/metadata-team/wiki>__

How to build @@@@@@@@@@@@

See INSTALL.rst <INSTALL.rst>__ for instructions on how to build the schemas and their documentation.

How to contribute changes @@@@@@@@@@@@@@@@@@@@@@@@@

See the CONTRIBUTING.rst <CONTRIBUTING.rst>__ document.

License @@@@@@@

See the LICENSE <LICENSE>__

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