BeaconResponse - a Perl CGI for Beacon+ queries on GA4GH compatible databases

Query parameters

• datasetId
  • the dataset to be queried
  • example: arraymap
  • default: arraymap
• assemblyId
  • the genome assembly
  • example: GRCh38

Database naming

The script uses some naming conventions for databases and collections:

• MongoDB database (in our implementation)
  • datasetId
• collections
  • individuals
  • biosamples
  • callsets
  • variants

Example use, web call:

SNV query on dataset "dipg"

• http://beacon.arraymap.org/beacon/beaconplus-server/beaconresponse.cgi?datasetId=dipg&referenceName=17&assemblyId=GRCh38&start=7733516&referenceBases=G&alternateBases=A&filters=icdot-C71.7

CNV query (defaults do dataset "arraymap") with bio-metadata component ("filters")

• http://beacon.progenetix.org/beacon/beaconplus-server/beaconresponse.cgi?datasetId=arraymap&referenceName=9&assemblyId=GRCh38&startMin=19,500,000&startMax=21,975,098&endMin=21,967,753&endMax=24,500,000&alternateBases=DEL&filters=ncit:C3224