Features

Variant Object Types

AnyVar enables the registration and retrieval of a number of different variation object types, beginning with core elements of the GA4GH Variation Representation Specification (VRS):

• VRS Allele

• VRS SequenceLocation

• VRS SequenceReference

Variant Translation

AnyVar implements a Translator abstraction that can be used to ingest free-text variation expressions of known nomenclatures. By way of the VRS-Python translator module, the following kinds of expressions are supported:

Expression Type	Example
HGVS	NC_000007.14:g.140753336A>T
SPDI	NC_000007.14:140753335:A:T
gnomAD/VCF	7-140753335-A-T

VCF Ingestion and Annotation

AnyVar can ingest and register all variants (and reference alleles) contained within a Variant Call Format (VCF) file, and return a file copy with variation IDs included as INFO field properties.

Object Annotations

Registered variation objects can be associated with annotations. Annotations consist of a type, of type str, and a value, which can be any JSON-serializable object or value. Annotations may be used to link to external references, indicate variant classifications, or otherwise adjoin genomic knowledge to a variation.

class anyvar.core.metadata.Annotation(**data)

Generic annotation class which attaches any object to an identifier

annotation_type: str

annotation_value: TypeAliasType

object_id: str

Variant Mappings

Mappings can be used to register specific modes of relationship between variations, such as reference assembly liftover. The VariationMappingType enum provides the supported kinds of relationships:

class anyvar.core.metadata.VariationMappingType(value)

Supported mapping types between VRS Variations.

LIFTOVER = 'liftover'

TRANSCRIPTION = 'transcription'

TRANSLATION = 'translation'

Stateless Mode

Optionally, an AnyVar server can be configured as stateless, to provide its variant translation and bulk file annotation functions without any persistent object registration backend. This utilizes the NoObjectStore class in place of a relational data backend.