GA4GH Variation Representation Specification
HEAD
Introduction
Quick Start
Concepts
Molecular Variation
Allele
Definition and Information Model
Example
Implementation Guidance
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 Variation
Copy Number Count
Copy Number Change
Locations and References
Sequence Location
Definition and Information Model
Example
Implementation Guidance
Sequence Reference
Definition and Information Model
Example
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
Primitive Types
Range
residue
sequenceString
Imported Classes
Entity
Element
Extension
Coding
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
What’s Next?
Releases
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
Decision-maker roles
Feature Developers
Product Implementers
Product Leads
Work Stream Leads
GA4GH Computed Identifier Alignment
Background
VRS Convention
GA4GH Digest Keys
GA4GH Type Prefixes
Administration
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
Glossary
GA4GH Variation Representation Specification
Appendices
View page source
Appendices
Class Diagram
GKS Maturity Model
Feature Maturity levels
Decision-maker roles
GA4GH Computed Identifier Alignment
Background
VRS Convention
GA4GH Type Prefixes
Truncated Digest Timing and Collision Analysis
Conclusions
Digest Timing
Collision Analysis
Choosing a digest size
Glossary