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Genomic Coordinates and Mappings

GA4GH Beacon Genome Coordinate Use Recommendation1

  • Beacon recommends the use of a "0-start, half-open" (interbase) coordinate system
  • "1-start, fully-closed" should be used when displaying coordinates through a Beacon GUI

Variant normalization

The Beacon v2 specification does not prescribe which style of variant normalization sequence defined queries are based on. In practice usually the VCF model is assumed (parsimony with avoidance of empty alleles). However, the GA4GH VRS specification argues against this practice and recommends a fully justified normalization2.

Beacon Scouts To Do

The Beacon Variant Scouts team will work on documenting a recommended variant normalization format which might deviate from current practices.

  1. Source: @andrewyatz at GenomeStandards ↩

  2. VRS normalization rules as design decision: Alleles are Fully Justified ↩