allele_annotation_service

************* /variantannotations ****************

This section will be re-instated when features are available in the API

Only return variant annotations for any of these features. Features may include specific transcripts or genes. A search by gene will return information for all transcripts associated with the gene in the variant annotation set. This or a location (referenceName/referenceId plus optional start and end) must be supplied. If empty, return all variant annotations in specified window. repeated string feature_ids;

************* /variantannotationsets ****************

SearchVariantAnnotationSets(request)
Parameters:requestSearchVariantAnnotationSetsRequest
Return type:SearchVariantAnnotationSetsResponse
Throws:GAException

Returns a list of available variant annotation sets.

POST /variantannotationsets/search must accept a JSON version of SearchVariantAnnotationSetsRequest as the post body and will return a JSON version of SearchVariantAnnotationSetsResponse.

SearchVariantAnnotations(request)
Parameters:requestSearchVariantAnnotationsRequest
Return type:SearchVariantAnnotationsResponse
Throws:GAException

Gets a list of VariantAnnotation messages matching the search criteria.

This allows the mining of allele-specific annotations on a VariantSet by either a region or by a set of genomic features. Where a region is supplied annotation of all alleles vs all features in the region is returned. Where a set of features is supplied, only annotations against these features (matching on featuretype and id) are returned and other overlapping features are ignored.

variantannotationsets/search returns information on the input to the annotation. This will be a VariantSet and the reference data and software versions used in calculating the annotation. It is essential this information is exhaustive.

POST /variantannotations/search must accept a JSON version of SearchVariantAnnotationsRequest as the post body and will return a JSON version of SearchVariantAnnotationsResponse.

GetVariantAnnotationSet(request)
Parameters:requestGetVariantAnnotationSetRequest
Return type:VariantAnnotationSet
Throws:GAException

Gets an VariantAnnotationSet by ID.

GET /variantannotationsets/{variant_annotation_set_id} will return a JSON version of VariantAnnotationSet.

message SearchVariantAnnotationsRequest
Fields:
  • variant_annotation_set_id (string) – Required. The ID of the variant annotation set to search over.
  • reference_name (string) – Only return variants with reference alleles on the reference with this name. One of this field or reference_id is required.
  • reference_id (string) – Only return variants with reference alleles on the reference with this ID. One of this field or reference_name is required.
  • start (long) – Required if reference_name or reference_id supplied. The beginning of the window (0-based, inclusive) for which variants with overlapping reference alleles should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
  • end (long) – Required if reference_name or reference_id supplied. The end of the window (0-based, exclusive) for which variants with overlapping reference alleles should be returned.
  • effects (list of OntologyTerm) – This filter allows variant, transcript combinations to be extracted by effect type(s). Only return variant annotations including any of these effects and only return transcript effects including any of these effects. Exact matching across all fields of the Sequence Ontology OntologyTerm is required. (A transcript effect may have multiple SO effects which will all be reported.) If empty, return all variant annotations.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of next_page_token from the previous response.

This request maps to the body of POST /variantannotations/search as JSON.

message SearchVariantAnnotationsResponse
Fields:
  • variant_annotations (list of VariantAnnotation) – The list of matching variant annotations.
  • next_page_token (string) – The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren’t any additional results.

This is the response from POST /variantannotations/search expressed as JSON.

message SearchVariantAnnotationSetsRequest
Fields:
  • variant_set_id (string) – Required. The VariantSet to search.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of next_page_token from the previous response.

This request maps to the body of POST /variantannotationsets/search as JSON.

message SearchVariantAnnotationSetsResponse
Fields:
  • variant_annotation_sets (list of VariantAnnotationSet) – The list of matching variant annotation sets.
  • next_page_token (string) – The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren’t any additional results.

This is the response from POST /variantannotationsets/search expressed as JSON.

message GetVariantAnnotationSetRequest
Fields:
  • variant_annotation_set_id (string) – The ID of the VariantAnnotationSet to be retrieved.

This request maps to the URL GET /variantannotationsets/{id}.