GA4GH variant

The document describes attributes of the variant object. In its current implementation, valiant (and related genomic objects such as callset) represent extended versions of the original, VCF-derived GA4GH schema. This format may be superseeded or augmented based on current developments in the GA4GH::GKS work stream.

The schema definitions are done in the YAML file.

Variant

Properties of the Variant class

Property	Type	Format	Description
alternate_bases	string		one or more bases relative to start position of the reference genome,replacing the reference_bases value; for precise variants
biosample_id			The identifier ("biosample.id") of the biosample this variant was reported from. This is a shortcut to using the variant -> callset -> biosample chaining.
callset_id	string		The identifier ("callset.id") of the callset this variant is part of.
created	string		The creation time of this record, in ISO8601
digest	string		concatenated unique specific elements of the variant
end	array	int64	array of 0 (for presise sequence variants), 1 or 2 (for imprecise end position of structural variant) integers
genotype	array		list of strings, which represent the (phased) alleles in which the variant was being observed
id	string		The local-unique identifier of this variant (referenced as "variant_id").
info			additional variant information, as defined in the example and accompanying documentation
mate_name	string		Mate name (chromosome) for fusion (BRK) events; otherwise left empty. Accepting values 1-22, X, Y.
reference_bases	string		one or more bases at start position in the reference genome, which have been replaced by the alternate_bases value; for precise variants
reference_name	string		Reference name (chromosome). Accepting values 1-22, X, Y.
start	array	int64	array of 1 or 2 (for imprecise end position of structural variant) integers
updated	string		The time of the last edit of this record, in ISO8601
variant_type	string		the variant type in case of a named (structural) variant (e.g. DUP, DEL, BRK ...)

Extended notes and examples on the Variant properties

alternate_bases

one or more bases relative to start position of the reference genome,replacing the reference_bases value; for precise variants

Example

'alternate_bases' : "AC"

biosample_id

The identifier (“biosample.id”) of the biosample this variant was reported from. This is a shortcut to using the variant -> callset -> biosample chaining.

Example

'biosample_id' : "pgx-bs-987647"

callset_id

The identifier (“callset.id”) of the callset this variant is part of.

Example

'callset_id' : "PGX_AM_CS_GSM1690424"

created

The creation time of this record, in ISO8601

Example

'created' : "2017-10-25T07:06:03Z"

digest

concatenated unique specific elements of the variant

Example

'digest' : "4:12282-46465:DEL"

end

array of 0 (for presise sequence variants), 1 or 2 (for imprecise end position of structural variant) integers

Example

'end' : [
  21977798,
  21978106
]

Queries:

the query will return all variants with any overlap of the CDKN2A CDR

db.variants.find( { "reference_name" : 9,  "variant_type" : "DEL", "start" : { $lteq : 21975098 }, "end" : { $gteq : 21967753 } } )

genotype

list of strings, which represent the (phased) alleles in which the variant was being observed

Example

'genotype' : [
  '1',
  '.'
]

id

The local-unique identifier of this variant (referenced as “variant_id”).

Example

'id' : "amvar-8754-7751-1119-8539"

info

additional variant information, as defined in the example and accompanying documentation

Example

'info' : {
  'cnv_value' : '-0.294',
  'cnv_length' : 1205290
}

mate_name

Mate name (chromosome) for fusion (BRK) events; otherwise left empty. Accepting values 1-22, X, Y.

Example

'mate_name' : 14

reference_bases

one or more bases at start position in the reference genome, which have been replaced by the alternate_bases value; for precise variants

Example

'reference_bases' : "G"

reference_name

Reference name (chromosome). Accepting values 1-22, X, Y.

Example

'reference_name' : 8

start

array of 1 or 2 (for imprecise end position of structural variant) integers

Example

'start' : [
  20867740
]

updated

The time of the last edit of this record, in ISO8601

Example

'updated' : "2022-11-11T09:45:13Z"

variant_type

the variant type in case of a named (structural) variant (e.g. DUP, DEL, BRK …)

Example

'variant_type' : "DEL"