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

Properties

alternateBases

• type: string

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 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) are be represented in variantType.

Either alternateBases or variantType is required.

alternateBases Value Example

assemblyId

• type: string

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

assemblyId Value Example

"GRCh38"

datasetIds

• type: array of string

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

• type: integer

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

end Value Example

5556

mateName

• type: https://beacon-project.io/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]

Second chromosome in fusion events, as string

mateName Value Examples

"22"

"Y"

referenceBases

• type: string

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

• type: https://beacon-project.io/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]

Chromosome as string

referenceName Value Examples

"22"

"Y"

start

• type: integer (int64)

Start position of the range in which to match overlapping variants

• 0-based, inclusive

start Value Examples

0

6298005

variantType

• type: string

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

Examples:

• DUP: duplication of sequence following start; not necessarily in situ
• DEL: deletion of sequence following start
• BND: breakend, i.e. termination of the allele at position start or in the startMin => startMax interval, or fusion of the sequence to distant partner

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"
}