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ga4gh / ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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Extending the variant model for DUP, DEL structural variants #772

Closed mbaudis closed 7 years ago

mbaudis commented 7 years ago

This is a first attempt to address the need for representation of structural variants. It is chiefly aimed to encode sequence duplications/deletions, and follows examples from VCFv4.2. The first commit does not yet implement the services part or documentation.

For some of the discussions, please see issue https://github.com/ga4gh/schemas/issues/752 .

david4096 commented 7 years ago

Awesome @mbaudis! Looking forward to working with this in practice. Being able to easily interpret the type of the variant always seemed a useful canonical field to me! What do you think of making the type an enumeration as opposed to a string?

mbaudis commented 7 years ago

@david4096 I am neutral regarding enum vs. string; both need some way to document permitted values. This is mostly a schema design decision (we've been going back and forth, with the first version having enums, then those being discouraged ...).

For the code integration team to edit/decide (so go ahead ...).

david4096 commented 7 years ago

Closed in favor of https://github.com/ga4gh/schemas/pull/827