Type: object
Description: CNV request against Beacon resources.

TODO: The documented queries will fail current tests due to the lack of the referenceBases parameter.

Properties

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"
]

endMax

• type: integer (int64)

Maximum end coordinate. See startMin.

endMax Value Examples

344452

244238579

endMin

• type: integer (int64)

Minimum end coordinate. See startMin.

endMin Value Examples

34

244238578

includeDatasetResponses

• type: string

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

referenceName

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

Chromosome as string

referenceName Value Examples

"22"

"Y"

startMax

• type: integer (int64)

Maximum start coordinate. See startMin.

startMax Value Examples

6298006

243998770

startMin

• type: integer (int64)

Minimum start coordinate

• startMin + startMax + endMin + endMax
• for querying imprecise positions (e.g. identifying all structural variants starting anywhere between startMin <-> startMax, and ending anywhere between endMin <-> endMax)
• single or double sided precise matches can be achieved by setting startMax = startMin+1 XOR endMax = endMin+1 (0-based, interbase coordinates)

startMin Value Examples

0

6298005

variantType

• type: string

The variantType is used to denote the type of structural variant.

Use in BeaconCnvRequest:

• DUP: duplication of sequence following start; not necessarily in situ
• DEL: deletion of sequence following start
• CNV: either DUP or DEL or CNV

variantType Value Examples

"DUP"

"DEL"

BeaconCnvRequest Value Example

{
   "assemblyId" : "GRCh38",
   "datasetIds" : [
      "arraymap",
      "progenetix"
   ],
   "endMax" : "26000000",
   "endMin" : "21967753",
   "referenceName" : "9",
   "startMax" : "21975098",
   "startMin" : "18000000",
   "variantType" : "DEL"
}