ga4gh-schemas

.. 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
__ is an international coalition,
formed to enable the sharing of genomic and clinical data.

The 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
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The Reads Task
Team __ 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 __ 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 __ 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
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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
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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
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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 __.

Metadata Task Team
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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 __

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

How to contribute changes
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See the CONTRIBUTING.rst __ document.

License
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See the LICENSE __

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