BeaconSnvRequest [beacon ]

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

Attributes

Type: object
Description: The precise SNV query subtype of the BeaconAlleleRequest.

Properties

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

alternateBases

The bases that appear instead of the reference bases, as described for referenceBases.

Symbolic ALT alleles (DEL, INS, DUP, INV, CNV, DUP:TANDEM, DEL:ME, INS:ME) cannot be represented in alternateBases.

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"
]

includeDatasetResponses

Indicator of whether responses for individual datasets (datasetAlleleResponses) should be included in the response (BeaconAlleleResponse) to this request or not. If null (not specified), the default value of NONE is assumed.

includeDatasetResponses Value Example

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). For the precise BeaconSnvRequest, only the start parameter is being used.

start Value Examples
0
6298005

BeaconSnvRequest Value Example

{
   "alternateBases" : "A",
   "assemblyId" : "GRCh38",
   "datasetIds" : [
      "dipg",
      "progenetix"
   ],
   "includeDatasetResponses" : "HIT",
   "referenceBases" : "G",
   "referenceName" : "17",
   "start" : "7577121"
}