Warning
THIS IS NOT THE OFFICIAL GA4GH VRS DOCUMENTATION! This is a demonstration build for discussing advancements to the maturity model and versioning system for GKS specification development. Please refer to https://vrs.ga4gh.org for the GA4GH VRS standard.
1.2¶
1.2.0¶
News¶
The first manuscript for VRS has been submitted. Please cite https://www.biorxiv.org/content/10.1101/2021.01.15.426843v1.
Want to get involved? See the VRS Appendix for the many ways that you can inform and contribute to VRS.
Important¶
SimpleInterval and SequenceState are deprecated. They will be removed in VRS 2.0.
Major Changes¶
New classification of variation types.
Molecular Variation refers to variation within or of a contiguous molecule
Systemic Variation refers to variation in the context of a system, such as a genome, sample, or homologous chromosomes
UtilityVariation classes provide useful representations for certain technical operations
New SequenceExpressions subclasses replace SequenceState. Subtypes are:
DerivedSequenceExpression, which representations sequence notionally derived from a SequenceLocation
RepeatedSequenceExpression, which represents contiguous repeats of a sequence
LiteralSequenceExpression, which wraps a Sequence and provides data structure parity with other SequenceExpressions
CopyNumberCount, a form of SystemicVariation, represents the copies of a molecule within a genome, and can be used to express concepts such as amplification and copy loss.
Gene enables reference to an external definition of a gene, particularly for useas a subject of copy number expressions.
DefiniteRange and IndefiniteRange represent bounded and half-bounded ranges respectively. A new Number type wraps integers so that some attributes may assume values of any of these three types.