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Beacon CNV Queries

Beacon Project Query Documentation

The Beacon project's documentation includes examples for current queries enabling discovery of CNVs (in resources supporting these formats).

Bracket queries

Beacon parameters

  • In principle the assemblyId should not be needed if specifying the refseq ID
  • Most beacons probably would go for assemblyId + chromosome-style referenceName (e.g. 9)
"g_variant": {
    "assemblyId": "GRCh38",
    "end": [21967753, 22500000],
    "referenceName": "refseq:NC_000009.12",
    "start": [21500000, 21975098],
    "variantType": "EFO:0030067"
}

?assemblyId=GRCh38&referenceName=refseq:NC_000009.12&start=21500000,21975098&end=21967753,22500000&variantType=EFO:0030067

MongoDB translation

The parameters in the MongoDB query represent a "VRSified standard model" structure - YMMV. Also, this example shows the expansion of the basic "deletion" code (EFO:0030067) into all its child terms.

{
    "$and": [
        {"location.sequence_id": "refseq:NC_000009.12"},
        {"location.start": {"$gte": 21500000}},
        {"location.start": {"$lt": 21975098}},
        {"location.end": {"$gte": 21967753}},
        {"location.end": {"$lt": 22500000}},
        {"variantState.id": {
                "$in": [
                    "EFO:0030067",
                    "EFO:0030068",
                    "EFO:0020073",
                    "EFO:0030069"
                ]
            }
        }
    ]
}