Lines Matching full:variant
44 // Creates variant data by asynchronously importing the provided information.
46 // For the definitions of variant sets and other genomics resources, see
50 // The variants for import will be merged with any existing variant that
52 // alternative bases. If no such variant exists, a new one will be created.
54 // When variants are merged, the call information from the new variant
55 // is added to the existing variant, and Variant info fields are merged
61 // Imported VCF headers are appended to the metadata already in a variant set.
70 // Creates a new variant set.
72 // For the definitions of variant sets and other genomics resources, see
76 // The provided variant set must have a valid `datasetId` set - all other
86 // Exports variant set data to an external destination.
88 // For the definitions of variant sets and other genomics resources, see
99 // Gets a variant set by ID.
101 // For the definitions of variant sets and other genomics resources, see
110 // Returns a list of all variant sets matching search criteria.
112 // For the definitions of variant sets and other genomics resources, see
126 // Deletes a variant set including all variants, call sets, and calls within.
129 // For the definitions of variant sets and other genomics resources, see
139 // Updates a variant set using patch semantics.
141 // For the definitions of variant sets and other genomics resources, see
166 // Creates a new variant.
171 rpc CreateVariant(CreateVariantRequest) returns (Variant) {
174 body: "variant"
178 // Updates a variant.
184 // This method supports patch semantics. Returns the modified variant without
186 rpc UpdateVariant(UpdateVariantRequest) returns (Variant) {
189 body: "variant"
193 // Deletes a variant.
204 // Gets a variant by ID.
209 rpc GetVariant(GetVariantRequest) returns (Variant) {
221 // Each variant will be
222 // merged with an existing variant that matches its reference sequence,
223 // start, end, reference bases, and alternative bases. If no such variant
226 // When variants are merged, the call information from the new variant
227 // is added to the existing variant. Variant info fields are merged as
235 // suppose you were trying to merge a new variant with an existing one and
239 // // Existing variant - irrelevant fields trimmed for clarity
260 // // New variant with conflicting call information
281 // The resulting merged variant would overwrite the existing calls with those
282 // from the new variant:
377 // Metadata describes a single piece of variant call metadata.
423 // A variant set is a collection of call sets and variants. It contains summary
424 // statistics of those contents. A variant set belongs to a dataset.
429 // The dataset to which this variant set belongs.
432 // The server-generated variant set ID, unique across all variant sets.
435 // The reference set to which the variant set is mapped. The reference set
436 // describes the alignment provenance of the variant set, while the
437 // `referenceBounds` describe the shape of the actual variant data. The
441 // For example, given a variant set that is mapped to the GRCh38 reference set
442 // and contains a single variant on reference 'X', `referenceBounds` would
447 // A list of all references used by the variants in a variant set
451 // The metadata associated with this variant set.
457 // A textual description of this variant set.
461 // A variant represents a change in DNA sequence relative to a reference
462 // sequence. For example, a variant could represent a SNP or an insertion.
463 // Variants belong to a variant set.
468 // Each of the calls on a variant represent a determination of genotype with
469 // respect to that variant. For example, a call might assign probability of 0.32
473 message Variant { message
474 // The ID of the variant set this variant belongs to.
477 // The server-generated variant ID, unique across all variants.
480 // Names for the variant, for example a RefSNP ID.
483 // The date this variant was created, in milliseconds from the epoch.
486 // The reference on which this variant occurs.
490 // The position at which this variant occurs (0-based).
494 // The end position (0-based) of this variant. This corresponds to the first
500 // The reference bases for this variant. They start at the given
507 // A measure of how likely this variant is to be real.
511 // A list of filters (normally quality filters) this variant has failed.
512 // `PASS` indicates this variant has passed all filters.
515 // A map of additional variant information. This must be of the form
519 // The variant calls for this particular variant. Each one represents the
520 // determination of genotype with respect to this variant.
525 // variant. It may include associated information such as quality and phasing.
529 // The ID of the call set this variant call belongs to.
532 // The name of the call set this variant call belongs to.
535 // The genotype of this variant call. Each value represents either the value
537 // `alternateBases`. If a variant had a `referenceBases`
541 // represented the heterozygous value `CA` for this variant.
549 // If this field is present, this variant call's genotype ordering implies
550 // the phase of the bases and is consistent with any other variant calls in
556 // The genotype likelihoods for this variant call. Each array entry
564 // A map of additional variant call information. This must be of the form
569 // A call set is a collection of variant calls, typically for one sample. It
570 // belongs to a variant set.
584 // The IDs of the variant sets this call set belongs to. This field must
585 // have exactly length one, as a call set belongs to a single variant set.
606 // variant in the reference sequence.
610 // The variant data import request.
615 // VCF (Variant Call Format). The VCF files may be gzip compressed. gVCF is
624 // Required. The variant set to which variant data should be imported.
627 // A list of URIs referencing variant files in Google Cloud Storage. URIs can
633 // The format of the variant data being imported. If unspecified, defaults to
653 // The variant data import response.
661 // Required. The variant set to be created. Must have a valid `datasetId`.
665 // The variant data export request.
674 // Required. The ID of the variant set that contains variant data which
675 // should be exported. The caller must have READ access to this variant set.
678 // If provided, only variant call information from the specified call sets
679 // will be exported. By default all variant calls are exported.
700 // The variant set request.
702 // Required. The ID of the variant set.
706 // The search variant sets request.
708 // Exactly one dataset ID must be provided here. Only variant sets which
722 // The search variant sets response.
724 // The variant sets belonging to the requested dataset.
733 // The delete variant set request.
735 // The ID of the variant set to be deleted.
740 // The ID of the variant to be updated (must already exist).
743 // The new variant data. Only the variant_set.metadata will be considered
758 // The variant search request.
760 // At most one variant set ID must be provided. Only variants from this
761 // variant set will be returned. If omitted, a call set id must be included in
768 // Only return variant calls which belong to call sets with these ids.
769 // Leaving this blank returns all variant calls. If a variant has no
794 // limit may be exceeded in the event that a matching variant contains more
800 // The variant search response.
803 repeated Variant variants = 1;
812 // The variant to be created.
813 Variant variant = 1; field
817 // The ID of the variant to be updated.
820 // The new variant data.
821 Variant variant = 2; field
824 // fields are [names][google.genomics.v1.Variant.names] and
825 // [info][google.genomics.v1.Variant.info]. Acceptable values are "names" and
831 // The ID of the variant to be deleted.
836 // The ID of the variant.
841 // The destination variant set.
845 repeated Variant variants = 2;
854 // Restrict the query to call sets within the given variant sets. At least one
919 // The variant set ID from which to stream variants.
922 // Only return variant calls which belong to call sets with these IDs.
923 // Leaving this blank returns all variant calls.
939 repeated Variant variants = 1;
942 // Operations to be performed during import on Variant info fields.
949 // By default, Variant info fields are persisted if the Variant doesn't
950 // already exist in the variantset. If the Variant is equivalent to a
951 // Variant already in the variantset, the incoming Variant's info field
952 // is ignored in favor of that of the already persisted Variant.
955 // This operation removes an info field from the incoming Variant
956 // and persists this info field in each of the incoming Variant's Calls.