{S}[B] Status [i] | proposal |
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Provenance | |
Used by | |
Contributors |
|
Source (v1.1.0) |
Type: object
Description: A BeaconAlleleRequest
flavour for matching variants in a genomic range.
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 |
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 ExampleAssembly identifier (GRC notation, e.g. GRCh37
).
assemblyId
Value Example"GRCh38"
Identifiers of datasets, as defined in BeaconDataset
. If this
field is null/not specified, all datasets should be queried.
datasetIds
Value Example[
"arraymap",
"TCGA"
]
Start position of the range in which to match overlapping variants. See start.
end
Value Example5556
Second chromosome in fusion events, as string
mateName
Value Examples"22"
"Y"
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 ExampleChromosome as string
referenceName
Value Examples"22"
"Y"
Start position of the range in which to match overlapping variants
start
Value Examples0
6298005
The variantType
is used to denote e.g. structural variants.
Examples:
start
; not necessarily in
situstart
start
or in the startMin
=> startMax
interval, or fusion
of the sequence to distant partnerEither 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"
}