BeaconAlleleRequest [beacon ]

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.1.0)

Attributes

Type: object
Description: Allele request as interpreted by the beacon.

Properties

Property Type
alternateBases string
assemblyId string
datasetIds array of string
end integer
endMax integer
endMin integer
mateName https://beacon-project.io/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
referenceBases string
referenceName https://beacon-project.io/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
start integer (int64)
startMax integer
startMin integer
variantType string

alternateBases

The bases that appear instead of the reference bases. Accepted values: [ACGTN]*. N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. For example a sequence where the first and last bases are known, but the middle portion can exhibit countless variations of [ACGT], or the bases are unknown: ANNT the Ns can take take any form of [ACGT], which makes both ACCT and ATGT (or any other combination) viable sequences.

Symbolic ALT alleles (DEL, INS, DUP, INV, CNV, DUP:TANDEM, DEL:ME, INS:ME) will be represented in variantType.

Optional: either alternateBases or variantType is required.

alternateBases Value Example

assemblyId

Assembly identifier (GRC notation, e.g. GRCh37).

assemblyId Value Example
"GRCh38"

datasetIds

Identifiers of datasets, as defined in BeaconDataset. If this field is null/not specified, all datasets should be queried.

datasetIds Value Example
[
   "arraymap",
   "TCGA"
]

end

Precise end coordinate (0-based, exclusive). See start.

end Value Example
5556

endMax

Maximum end coordinate. See startMin.

endMax Value Examples
344452
244238579

endMin

Minimum end coordinate. See startMin.

endMin Value Examples
34
244238578

mateName

Second chromosome in fuion events, as string

mateName Value Examples
"22"
"Y"

referenceBases

Reference bases for this variant (starting from start). Accepted values: [ACGTN]*. N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. For example a sequence where the first and last bases are known, but the middle portion can exhibit countless variations of [ACGT], or the bases are unknown: ANNT the Ns can take take any form of [ACGT], which makes both ACCT and ATGT (or any other combination) viable sequences.

referenceBases Value Example

referenceName

Chromosome as string

referenceName Value Examples
"22"
"Y"

start

Precise start coordinate position, allele locus (0-based, inclusive).

start Value Examples
0
6298005

startMax

Maximum start coordinate. See startMin.

startMax Value Examples
6298006
243998770

startMin

Minimum start coordinate

startMin Value Examples
0
6298005

variantType

The variantType is used to denote e.g. structural variants.

Examples:

Optional: either alternateBases or variantType is required.

variantType Value Examples
"DUP"
"DEL"

BeaconAlleleRequest Value Examples

{
   "assemblyId" : "GRCh38",
   "datasetIds" : [
      "arraymap",
      "progenetix"
   ],
   "endMax" : "26000000",
   "endMin" : "21967753",
   "referenceBases" : "N",
   "referenceName" : "9",
   "startMax" : "21975098",
   "startMin" : "18000000",
   "variantType" : "DEL"
}
{
   "alternateBases" : "A",
   "assemblyId" : "GRCh38",
   "datasetIds" : [
      "dipg"
   ],
   "referenceBases" : "G",
   "referenceName" : "17",
   "start" : "7577121"
}
2020-06-23