ga4gh-beacon
Catalogue of query examples
Especially with the upcoming filters, but for CNV, wild card and range matches, we need to provide a catalogue of query examples supported through the current protocol version (and then w/ added options in the developer branch).
There has also been a specific request from the GA4GH GKS VarRep group, to match Beacon needs against the variant format(s) being developed there and how this matches to the {S}[B] variant proposal.
These are the current examples we use for Beacon+. It would be nice to have them reviewed/fixed (we have a custom back end).
Standard precise Beacon variant query
?datasetIds=dipg&referenceName=17&assemblyId=GRCh38&start=7577121&referenceBases=G&alternateBases=A
Structural variant query with fuzzy ends
This query matches deletions in the CDR of the CDKN2A locus, limiting to matches that have
- any overlap with the queried region
- are "focal"; i.e. both start and end of the deleted region cannot be > ~3Mbp from the locus
- additional: a filter using a private ontology term
?datasetIds=arraymap&referenceName=9&assemblyId=GRCh38&variantType=DEL&startMin=18000000&startMax=21975098&endMin=21967753&endMax=26000000&filters=pgx:icdom-94403
Wildcard/range query for "precise" events
This query targets any precise (i.e., annotated by referenceBases and alternateBases) vvariant in the CDR of the EIF4A1 gene.
However, since the current alternateBases does not allow for wildcard use (only N is possible), the query will only return matches with alternateBases of length 1.
?datasetIds=dipg&referenceName=17&assemblyId=GRCh38&startMin=7572826&endMax=7579005&referenceBases=*&alternateBases=N
Breakend search
The example queries for a break end (BND) at the MYC locus, w/o a specified translocation partner ("mate").
?datasetIds=arraymap&referenceName=8&assemblyId=GRCh38&variantType=BND&startMin=127500000&startMax=127900000