Pages tagged "faq"


Precise Variants

Precise variants are such with annotated sequences of 0….n length, and bases of [ATCGN] for the referenceBases and alternateBases attributes (N for “not specified”).

mbaudis, 2018-10-17: more ...

Range Queries and Structural Variants

The adoption of

  • variantType
  • startMin, startMax
  • endMin, endMax

into the Beacon v0.4 release enabled the execution of

  • range queries
  • fuzzy position matching
  • arbitrary sequence variants (though limited through supported & documented vocabularies)

mbaudis, 2018-10-17: more ...

Coordinate use for Beacon Queries

The coordinate system that should be used throughout GA4GH standards is 0-based half open.

mbaudis, 2018-10-17: more ...

What is a Beacon?

A Beacon is an online web service that allows users to query an institution’s databases, to determine whether they contain a genetic variant of interest. The query is structured as a yes/no question of the form: “Do you have any genomes with an ‘X’ at position Y on chromosome Z?”

mbaudis, 2018-10-17: more ...

What is the Beacon Project doing to mitigate the possibility and likelihood of reidentification through Beacons?

Any publica data resource containing “human derived” data has a potential for re-identification attacks, that is the identification of individuals contributing data to the resource.

Since its inception, the Beacon Project has been actively working with experts in GA4GH’s membership to address potential privacy concerns.

mbaudis, 2018-10-17: more ...