BeaconGenomicVariant beacon

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Source (v0.0.1)

Attributes

Type: object
Description: The document describes attributes of the BeaconGenomicVariant object. In its current implementation, BeaconGenomicVariant (and related genomic objects such as callset) represent extended versions of the original, VCF-derived GA4GH variant schema.

Compared to the VCF model it was derived from, this schema includes some changes:

This format may be superseeded or augmented based on current developments in the GA4GH::GKS work stream.

Properties

Property Type
alternateBases array of "string"
biosampleId string
callsetId string
digest string
end array of "int64"
genotype array of "string"
id string
info object
mateName https://schemablocks.org/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
referenceBases string
referenceName https://schemablocks.org/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
start array of "int64"
variantType string

alternateBases

TODO: Redefine for single-allele use?

alternateBases Value Examples
[
   "C"
]
[
   "TA",
   "TAA"
]

biosampleId

The optional identifier (“biosample.id”) of the biosample this variant was reported from. This is a shortcut to variant -> callset -> biosample chaining or replaces this in data models w/o separate callset level.

biosampleId Value Example
"pgx-bs-987647"

callsetId

callsetId Value Example
"PGX_AM_CS_GSM1690424"

digest

digest Value Example
"4:12282-46465:DEL"

end

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

end Value Example
[
   "21977798",
   "21978106"
]

genotype

The genotype parameter is largely redundant for single-sample variant annotations in contrast to VCF, where the alternat_bases calls have to be indicated for multiple callsets.

TODO: Remove for single-allele definition of BeaconGenomicVariant?

genotype Value Examples
[
   "1",
   "."
]
[
   "2",
   "1"
]

id

id Value Example
"amvar-8754-7751-1119-8539"

info

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

info Value Example
{
   "cnv_length" : "1205290",
   "cnv_value" : "-0.294"
}

mateName

Mate name (chromosome) for fusion (BND) events; otherwise left empty. Accepting values 1-22, X, Y. Compared to the VCF specification, where a fusion is defined from 2 BND variants and verbose annotations for describing fusion partners, the use of the mate_name attribute allows to treat fusion events as single “variant”. Conventions:

mateName Value Examples
"14"
"18"

referenceBases

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

referenceBases Value Example
"G"

referenceName

Chromosome as string

referenceName Value Examples
"22"
"Y"

start

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

start Value Example
[
   "20867740"
]

variantType

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

variantType Value Example
"DEL"

BeaconGenomicVariant Value Examples

{
   "alternate_bases" : [
      "AC",
      "ACC"
   ],
   "callset_id" : "DIPG_CS_0290",
   "digest" : "2:203420136:A>AC,ACC",
   "genotype" : [
      "2",
      "1"
   ],
   "id" : "5be1840772798347f0ed9e8b",
   "reference_bases" : "A",
   "reference_name" : "2",
   "start" : [
      "203420136"
   ]
}
{
   "biosample_id" : "fcl-bs-0099615",
   "callset_id" : "structdb-cs-nhl-0009876",
   "digest" : "8,14:20867740-21977798,21978106:BND",
   "end" : [
      "21977798",
      "21978106"
   ],
   "id" : "structdb-var-123456789",
   "mate_name" : "14",
   "reference_bases" : "N",
   "reference_name" : "8",
   "start" : [
      "20867740"
   ],
   "variant_type" : "BND"
}
{
   "callset_id" : "structdb-cs-nhl-0009876",
   "digest" : "6:63450000,63550000-63450000,63550000:DEL",
   "end" : [
      "63450000",
      "63550000"
   ],
   "id" : "structdb-var-123456790",
   "info" : {
      "cnv_length" : "85500000",
      "cnv_value" : "-0.294"
   },
   "reference_bases" : "N",
   "reference_name" : "6",
   "start" : [
      "63450000",
      "63550000"
   ],
   "variant_type" : "DEL"
}