The Beacon+ interface currently implements structural variant requests (i.e. DUP, DEL; see Beacon Github PR #94), in addition to standard Beacon SNV calls.
Code for the project is accessible through the Progenetix Github repository:
The latest version (2017-10-05) also adds an experimental support for biocharacteristics queries, against ontology term_ids as specified in the metadata development branch. This is mostly intended for development purposes - no documentation yet, besides the GA4GH notes.
The CNV example tests the Beacon+ UI and backend against the DIPG/pHGG dataset, with a range query looking for deletions involving the CDKN2A locus in a "focal" manner. The bracketing of start and end ranges will return deletions of less than ~5Mb, all at least partially overlapping the CDKN2A CDR (isoform 1).
Additionally, results from the variant query are then limited to callsets derived from biosamples of brain stem gliomas, as identified through the annotation of an icdot:c71.7 ICD-O topography term_id.
The SNV example test the Beacon+ UI and backend against the DIPG dataset, with a specific mutation.
|Dataset||Assembly||Chro||Var Type||Start Range||End Range||Pos||Ref