Example Queries

This page gives examples for query strings against Beacon implementations. This documentation is expected to be expanded over time, with adjustments for the expanding protocol options.

Beacon v1.1

Standard Precise Variant Queries (original “BeaconAlleleRequest”)

Standard “BeaconAlleleRequest” queries use a start position parameter (corresponding to VCF POS), corresponding referenceBases and the variant’s alternateBases.

referenceName referenceBases alternateBases variantType start end startMin startMax endMin endMax
required required required - required - - - - -
17 G A   7577120          

The example is against a variant observed in the EIF4A1 gene, as somatic mutation e.g. in childhood brain tumors.

Please be aware of the use of interbase coordinates in Beacon queries; i.e. the “human readable” 1-based position (chr17:7577121) is shifted to chr17:7577120.

referenceName=17&start=7577120&referenceBases=G&alternateBases=A

The complete query example includes the required datasetIds and assemblyId parameters:

referenceName=17&assemblyId=GRCh38&start=7577120&referenceBases=G&alternateBases=A

CNV Queries

The Beacon specification from 0.4 onwards allows the use of precise and “fuzzy” matches for CNV regions. However:

referenceName referenceBases alternateBases variantType start end startMin startMax endMin endMax
required required* - required - - required required required required
9 N   DEL     18000000 21975098 21967753 26000000

(* as of v1.1.0, the specification still requires a value in referenceBases. This can be skirted by using the N value.)

The example here shows a CNV query as implemented in Beacon+. It queries for CNVs (DEL) with any overlap of the CDKN2A CDR.

variantType=DEL&referenceName=9&startMin=18000000&startMax=21975098&endMin=21967753&endMax=26000000&referenceBases=N

More about the construction of such region overlap queries can be found in the “range queries” document.

More Documentation

@mbaudis 2019-09-24
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