BeaconRangeRequest [beacon ]

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

Attributes

Type: object
Description: A BeaconAlleleRequest flavour for matching variants in a genomic range.

Properties

Property Type
alternateBases string
assemblyId string
datasetIds array of string
end 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)
variantType string

alternateBases

The bases that appear instead of the reference bases.

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

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

Start position of the range in which to match overlapping variants. See start.

end Value Example
5556

mateName

Second chromosome in fusion 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

Start position of the range in which to match overlapping variants

start Value Examples
0
6298005

variantType

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

Examples:

Either alternateBases or variantType is required.

variantType Value Examples
"DUP"
"DEL"

BeaconRangeRequest Value Example

{
   "alternateBases" : "N",
   "assemblyId" : "GRCh38",
   "datasetIds" : [
      "dipg"
   ],
   "end" : "7579005",
   "referenceBases" : "N",
   "referenceName" : "17",
   "start" : "7572826"
}