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 (2017-09-05) 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 DGV example test the Beacon+ UI and backend against a subset of data from the Database of Genome Variants. The example here performs a base-specific match on one of the variants provided to us. Using the link to the UCSC browser provided in the results table will display the matching genome region, with more overlapping DGV entries (you may have to activate the DCV track for seeing them).
Since the data in DGV provides aggregated call counts per variant, the results differ from the strictly sample based examples:
The CNV example test the Beacon+ UI and backend against the arrayMap database, 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 malignant melanomas, as identified through the annotation of an ncit:c3224 NCIt Neoplasm Core term_id.
The SNV example test the Beacon+ UI and backend against the DIPG dataset, with a specific mutation.
|Dataset||Assembly||Chro||Start Range||End Range||Pos||Ref
Alt | Type