A Genomics Alliance Beacon, see http://ga4gh.org/#/beacon
* REST endpoint cgi-bin/beacon/info:
Shows info about beacon, e.g. number of variants served.
No parameters
* REST endpoint cgi-bin/beacon/query:
Parameters:
- chromosome: 1 - 22, X, Y or M
- alternateBases: A,C,T,G or I or D.
- position: position on chromosome. Depending on the default configuration, you need the optional parameter [positionBased]
- dataset: Optional. If not specified all datasets will be queried.
- reference: Optional. If specified, has to be GRCh37
- format: Optional. If "text", does not return JSON, but just one of the words "true", or "false". Easier to parse for shell scripts.
- positionBased: Optional. Type of nomenclature of the requested chromosome position. You can define the type of nomenclature used in the [position] parameter.
Values: 0 or 1
Important !!! : 1-based is the format that is stored the position on chromosome
is the DEFAULT format that the sistem use to the position on chromosome
Examples:
- 0-based is the DEFAULT format that the sistem use to the position on chromosome
query?chromosome=6&position=136597261&alternateBases=C
query?chromosome=6&position=136597261&alternateBases=C&format=text
query?chromosome=6&position=136597261&alternateBases=C&format=text&positionBased=0
query?chromosome=6&position=136597262&alternateBases=C&format=text&positionBased=1
- returns "true", this allele is in the beacon
query?chromosome=1&position=10149&alternateBases=A
query?chromosome=1&position=10149&alternateBases=A&positionBased=0
query?chromosome=1&position=10150&alternateBases=A&positionBased=1
- returns "false", this allele is not in the beacon
Examples:
- 1-based is the DEFAULT format that the sistem use to the position on chromosome
query?chromosome=6&position=136597262&alternateBases=C
query?chromosome=6&position=136597262&alternateBases=C&format=text
query?chromosome=6&position=136597261&alternateBases=C&format=text&positionBased=0
query?chromosome=6&position=136597262&alternateBases=C&format=text&positionBased=1
- returns "true", this allele is in the beacon
query?chromosome=1&position=10150&alternateBases=A
query?chromosome=1&position=10149&alternateBases=A&positionBased=0
query?chromosome=1&position=10150&alternateBases=A&positionBased=1
- returns "false", this allele is not in the beacon