GA4GH Variation Representation Specification Logo
  • Introduction
  • Quick Start
  • Concepts
    • Molecular Variation
      • Allele
        • Definition and Information Model
        • Example
        • Implementation Guidance
      • Relative Allele
        • Definition and Information Model
      • Adjacency
        • Definition and Information Model
        • Example
        • Implementation Guidance
      • Cis-Phased Block
        • Definition and Information Model
        • Example
      • Terminus
        • Definition and Information Model
        • Example
      • Derivative Molecule
        • Definition and Information Model
        • Components
        • Example
    • Systemic Variation
      • Copy Number Count
        • Definition and Information Model
        • Example
      • Copy Number Change
        • Definition and Information Model
        • Example
    • Locations and References
      • Location
        • Sequence Location
        • Relative Sequence Location
        • Sequence Offset Location
        • Sequence Reference
    • Sequence Expression
      • Literal Sequence Expression
        • Definition and Information Model
        • Example
      • Reference Length Expression
        • Definition and Information Model
        • Example
      • Length Expression
        • Definition and Information Model
        • Example
    • Additional Data Types
      • Abstract Classes
        • GA4GH Identifiable Object
        • Variation
        • Entity
        • Element
      • General Purposes Types
        • Extension
        • Mappable Concept
        • ConceptSet
        • Concept Mapping
        • Coding
      • Primitive Types
        • Range
        • residue
        • sequenceString
        • code
        • iriReference
  • Conventions
    • Required External Data
      • Contexts
      • Data Services
      • Suggested Implementation
        • Examples
    • Normalization
      • General Normalization Rules
      • Allele Normalization
        • LiteralSequenceExpression Alleles
      • Adjacency Normalization
    • Computed Identifiers
      • Requirements
      • Digest Serialization
      • Truncated Digest (sha512t24u)
      • Identifier Construction
      • References
    • Example
      • Translate HGVS to VRS
      • Generate a computed identifier
  • Examples
    • Splice-Adjacent HGVS Variant Examples
      • Splice acceptor — upstream intronic variant
        • HGVS expression
        • Transcript context
        • Transcript features at the splice junction
        • NCBI graphical sequence view
        • Anchor selection
        • Mapping relative to the anchor
        • Relative Allele representation
      • Splice acceptor — downstream intronic variant
        • HGVS expression
        • Transcript context
        • Transcript features at the splice junction
        • NCBI graphical sequence view
        • Anchor selection
        • Mapping relative to the anchor
        • Relative Allele representation
      • Splice donor — upstream intronic variant
        • HGVS expression
        • Transcript context
        • Transcript features at the splice junction
        • NCBI graphical sequence view
        • Anchor selection
        • Mapping relative to the anchor
        • Relative Allele representation
      • Splice donor — downstream intronic variant
        • HGVS expression
        • Transcript context
        • Transcript features at the splice junction
        • NCBI graphical sequence view
        • Anchor selection
        • Mapping relative to the anchor
        • Relative Allele representation
  • Releases
    • 2.0
      • 2.0.2
        • Summary of Changes
      • 2.0.1
        • Summary of Changes
      • 2.0.0
        • Major Changes
    • 1.3
      • 1.3.0
        • News
        • Major Changes
        • Minor Changes
    • 1.2
      • 1.2.0
        • News
        • Important
        • Major Changes
        • Minor Changes
    • 1.1
      • 1.1.2
      • 1.1.1
      • 1.1.0
        • New classes
        • Other data model changes
        • Documentation changes
    • 1.0
      • 1.0.0
  • Appendices
    • Class Diagram
    • GKS Maturity Model
      • Feature Maturity levels
        • Developing a Draft Product Feature
        • Advancing from Draft to Trial Use
        • Advancing from Trial Use to Normative
      • Product Versioning and Releases
        • Versioning examples
        • Releases
      • Decision-maker roles
        • Feature Developers
        • Product Implementers
        • Product Leads
        • Work Stream Leads
    • GA4GH Computed Identifier Alignment
      • Background
      • VRS Convention
        • GA4GH Inherent Properties
      • GA4GH Type Prefixes
        • Administration
    • Resource Identifiers
    • Truncated Digest Timing and Collision Analysis
      • Conclusions
      • Digest Timing
      • Collision Analysis
        • References
        • Background: The Birthday Problem
        • Approximation #1: Taylor approximation of terms of P’
        • Approximation #2: Taylor approximation of P’
        • Approximation #3: Square approximation
        • Summary of equations
      • Choosing a digest size
        • For completeness:
        • digest length (bytes) required for expected collision probability \(P\) over \(m\) messages
    • Design Decisions
      • GA4GH Inherent Properties over Value Objects
      • IRIs over CURIEs
      • IRI-References over IRIs
      • VRS identifier syntax and versioning
      • Inter-residue Coordinates
    • Glossary
GA4GH Variation Representation Specification
  • Examples
  • Edit on GitHub

Examples

This section guides users through real-world examples, illustrating how they can be modeled and represented using VRS.

  • Splice-Adjacent HGVS Variant Examples
    • Splice acceptor — upstream intronic variant
    • Splice acceptor — downstream intronic variant
    • Splice donor — upstream intronic variant
    • Splice donor — downstream intronic variant
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