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| <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variants.html">variants</a></h1> |
| <h2>Instance Methods</h2> |
| <p class="toc_element"> |
| <code><a href="#create">create(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Creates a new variant.</p> |
| <p class="toc_element"> |
| <code><a href="#delete">delete(variantId, x__xgafv=None)</a></code></p> |
| <p class="firstline">Deletes a variant.</p> |
| <p class="toc_element"> |
| <code><a href="#get">get(variantId, x__xgafv=None)</a></code></p> |
| <p class="firstline">Gets a variant by ID.</p> |
| <p class="toc_element"> |
| <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Creates variant data by asynchronously importing the provided information.</p> |
| <p class="toc_element"> |
| <code><a href="#merge">merge(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Merges the given variants with existing variants.</p> |
| <p class="toc_element"> |
| <code><a href="#patch">patch(variantId, body, x__xgafv=None, updateMask=None)</a></code></p> |
| <p class="firstline">Updates a variant.</p> |
| <p class="toc_element"> |
| <code><a href="#search">search(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Gets a list of variants matching the criteria.</p> |
| <p class="toc_element"> |
| <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> |
| <p class="firstline">Retrieves the next page of results.</p> |
| <h3>Method Details</h3> |
| <div class="method"> |
| <code class="details" id="create">create(body, x__xgafv=None)</code> |
| <pre>Creates a new variant. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="delete">delete(variantId, x__xgafv=None)</code> |
| <pre>Deletes a variant. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Args: |
| variantId: string, The ID of the variant to be deleted. (required) |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # A generic empty message that you can re-use to avoid defining duplicated |
| # empty messages in your APIs. A typical example is to use it as the request |
| # or the response type of an API method. For instance: |
| # |
| # service Foo { |
| # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); |
| # } |
| # |
| # The JSON representation for `Empty` is empty JSON object `{}`. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="get">get(variantId, x__xgafv=None)</code> |
| <pre>Gets a variant by ID. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Args: |
| variantId: string, The ID of the variant. (required) |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="import_">import_(body, x__xgafv=None)</code> |
| <pre>Creates variant data by asynchronously importing the provided information. |
| |
| For the definitions of variant sets and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| The variants for import will be merged with any existing variant that |
| matches its reference sequence, start, end, reference bases, and |
| alternative bases. If no such variant exists, a new one will be created. |
| |
| When variants are merged, the call information from the new variant |
| is added to the existing variant, and Variant info fields are merged |
| as specified in |
| infoMergeConfig. |
| As a special case, for single-sample VCF files, QUAL and FILTER fields will |
| be moved to the call level; these are sometimes interpreted in a |
| call-specific context. |
| Imported VCF headers are appended to the metadata already in a variant set. |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # The variant data import request. |
| "variantSetId": "A String", # Required. The variant set to which variant data should be imported. |
| "format": "A String", # The format of the variant data being imported. If unspecified, defaults to |
| # to `VCF`. |
| "sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can |
| # include wildcards [as described |
| # here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). |
| # Note that recursive wildcards ('**') are not supported. |
| "A String", |
| ], |
| "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to |
| # be performed on them. This is plumbed down to the MergeVariantRequests |
| # generated by the resulting import job. |
| "a_key": "A String", |
| }, |
| "normalizeReferenceNames": True or False, # Convert reference names to the canonical representation. |
| # hg19 haploytypes (those reference names containing "_hap") |
| # are not modified in any way. |
| # All other reference names are modified according to the following rules: |
| # The reference name is capitalized. |
| # The "chr" prefix is dropped for all autosomes and sex chromsomes. |
| # For example "chr17" becomes "17" and "chrX" becomes "X". |
| # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # This resource represents a long-running operation that is the result of a |
| # network API call. |
| "metadata": { # An OperationMetadata object. This will always be returned with the Operation. |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. |
| # programming environments, including REST APIs and RPC APIs. It is used by |
| # [gRPC](https://github.com/grpc). The error model is designed to be: |
| # |
| # - Simple to use and understand for most users |
| # - Flexible enough to meet unexpected needs |
| # |
| # # Overview |
| # |
| # The `Status` message contains three pieces of data: error code, error message, |
| # and error details. The error code should be an enum value of |
| # google.rpc.Code, but it may accept additional error codes if needed. The |
| # error message should be a developer-facing English message that helps |
| # developers *understand* and *resolve* the error. If a localized user-facing |
| # error message is needed, put the localized message in the error details or |
| # localize it in the client. The optional error details may contain arbitrary |
| # information about the error. There is a predefined set of error detail types |
| # in the package `google.rpc` that can be used for common error conditions. |
| # |
| # # Language mapping |
| # |
| # The `Status` message is the logical representation of the error model, but it |
| # is not necessarily the actual wire format. When the `Status` message is |
| # exposed in different client libraries and different wire protocols, it can be |
| # mapped differently. For example, it will likely be mapped to some exceptions |
| # in Java, but more likely mapped to some error codes in C. |
| # |
| # # Other uses |
| # |
| # The error model and the `Status` message can be used in a variety of |
| # environments, either with or without APIs, to provide a |
| # consistent developer experience across different environments. |
| # |
| # Example uses of this error model include: |
| # |
| # - Partial errors. If a service needs to return partial errors to the client, |
| # it may embed the `Status` in the normal response to indicate the partial |
| # errors. |
| # |
| # - Workflow errors. A typical workflow has multiple steps. Each step may |
| # have a `Status` message for error reporting. |
| # |
| # - Batch operations. If a client uses batch request and batch response, the |
| # `Status` message should be used directly inside batch response, one for |
| # each error sub-response. |
| # |
| # - Asynchronous operations. If an API call embeds asynchronous operation |
| # results in its response, the status of those operations should be |
| # represented directly using the `Status` message. |
| # |
| # - Logging. If some API errors are stored in logs, the message `Status` could |
| # be used directly after any stripping needed for security/privacy reasons. |
| "message": "A String", # A developer-facing error message, which should be in English. Any |
| # user-facing error message should be localized and sent in the |
| # google.rpc.Status.details field, or localized by the client. |
| "code": 42, # The status code, which should be an enum value of google.rpc.Code. |
| "details": [ # A list of messages that carry the error details. There will be a |
| # common set of message types for APIs to use. |
| { |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| ], |
| }, |
| "done": True or False, # If the value is `false`, it means the operation is still in progress. |
| # If true, the operation is completed, and either `error` or `response` is |
| # available. |
| "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="merge">merge(body, x__xgafv=None)</code> |
| <pre>Merges the given variants with existing variants. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Each variant will be |
| merged with an existing variant that matches its reference sequence, |
| start, end, reference bases, and alternative bases. If no such variant |
| exists, a new one will be created. |
| |
| When variants are merged, the call information from the new variant |
| is added to the existing variant. Variant info fields are merged as |
| specified in the |
| infoMergeConfig |
| field of the MergeVariantsRequest. |
| |
| Please exercise caution when using this method! It is easy to introduce |
| mistakes in existing variants and difficult to back out of them. For |
| example, |
| suppose you were trying to merge a new variant with an existing one and |
| both |
| variants contain calls that belong to callsets with the same callset ID. |
| |
| // Existing variant - irrelevant fields trimmed for clarity |
| { |
| "variantSetId": "10473108253681171589", |
| "referenceName": "1", |
| "start": "10582", |
| "referenceBases": "G", |
| "alternateBases": [ |
| "A" |
| ], |
| "calls": [ |
| { |
| "callSetId": "10473108253681171589-0", |
| "callSetName": "CALLSET0", |
| "genotype": [ |
| 0, |
| 1 |
| ], |
| } |
| ] |
| } |
| |
| // New variant with conflicting call information |
| { |
| "variantSetId": "10473108253681171589", |
| "referenceName": "1", |
| "start": "10582", |
| "referenceBases": "G", |
| "alternateBases": [ |
| "A" |
| ], |
| "calls": [ |
| { |
| "callSetId": "10473108253681171589-0", |
| "callSetName": "CALLSET0", |
| "genotype": [ |
| 1, |
| 1 |
| ], |
| } |
| ] |
| } |
| |
| The resulting merged variant would overwrite the existing calls with those |
| from the new variant: |
| |
| { |
| "variantSetId": "10473108253681171589", |
| "referenceName": "1", |
| "start": "10582", |
| "referenceBases": "G", |
| "alternateBases": [ |
| "A" |
| ], |
| "calls": [ |
| { |
| "callSetId": "10473108253681171589-0", |
| "callSetName": "CALLSET0", |
| "genotype": [ |
| 1, |
| 1 |
| ], |
| } |
| ] |
| } |
| |
| This may be the desired outcome, but it is up to the user to determine if |
| if that is indeed the case. |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { |
| "variantSetId": "A String", # The destination variant set. |
| "variants": [ # The variants to be merged with existing variants. |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| }, |
| ], |
| "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to |
| # be performed on them. |
| "a_key": "A String", |
| }, |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # A generic empty message that you can re-use to avoid defining duplicated |
| # empty messages in your APIs. A typical example is to use it as the request |
| # or the response type of an API method. For instance: |
| # |
| # service Foo { |
| # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); |
| # } |
| # |
| # The JSON representation for `Empty` is empty JSON object `{}`. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="patch">patch(variantId, body, x__xgafv=None, updateMask=None)</code> |
| <pre>Updates a variant. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| This method supports patch semantics. Returns the modified variant without |
| its calls. |
| |
| Args: |
| variantId: string, The ID of the variant to be updated. (required) |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| updateMask: string, An optional mask specifying which fields to update. At this time, mutable |
| fields are names and |
| info. Acceptable values are "names" and |
| "info". If unspecified, all mutable fields will be updated. |
| |
| Returns: |
| An object of the form: |
| |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="search">search(body, x__xgafv=None)</code> |
| <pre>Gets a list of variants matching the criteria. |
| |
| For the definitions of variants and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Implements |
| [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126). |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # The variant search request. |
| "end": "A String", # The end of the window, 0-based exclusive. If unspecified or 0, defaults to |
| # the length of the reference. |
| "pageSize": 42, # The maximum number of variants to return in a single page. If unspecified, |
| # defaults to 5000. The maximum value is 10000. |
| "start": "A String", # The beginning of the window (0-based, inclusive) for which |
| # overlapping variants should be returned. If unspecified, defaults to 0. |
| "maxCalls": 42, # The maximum number of calls to return in a single page. Note that this |
| # limit may be exceeded in the event that a matching variant contains more |
| # calls than the requested maximum. If unspecified, defaults to 5000. The |
| # maximum value is 10000. |
| "pageToken": "A 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 |
| # `nextPageToken` from the previous response. |
| "variantSetIds": [ # At most one variant set ID must be provided. Only variants from this |
| # variant set will be returned. If omitted, a call set id must be included in |
| # the request. |
| "A String", |
| ], |
| "variantName": "A String", # Only return variants which have exactly this name. |
| "referenceName": "A String", # Required. Only return variants in this reference sequence. |
| "callSetIds": [ # Only return variant calls which belong to call sets with these ids. |
| # Leaving this blank returns all variant calls. If a variant has no |
| # calls belonging to any of these call sets, it won't be returned at all. |
| "A String", |
| ], |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # The variant search response. |
| "nextPageToken": "A 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. |
| "variants": [ # The list of matching Variants. |
| { # A variant represents a change in DNA sequence relative to a reference |
| # sequence. For example, a variant could represent a SNP or an insertion. |
| # Variants belong to a variant set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # Each of the calls on a variant represent a determination of genotype with |
| # respect to that variant. For example, a call might assign probability of 0.32 |
| # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call |
| # belongs to a call set, which contains related calls typically from one |
| # sample. |
| "info": { # A map of additional variant information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "variantSetId": "A String", # The ID of the variant set this variant belongs to. |
| "end": "A String", # The end position (0-based) of this variant. This corresponds to the first |
| # base after the last base in the reference allele. So, the length of |
| # the reference allele is (end - start). This is useful for variants |
| # that don't explicitly give alternate bases, for example large deletions. |
| "calls": [ # The variant calls for this particular variant. Each one represents the |
| # determination of genotype with respect to this variant. |
| { # A call represents the determination of genotype with respect to a particular |
| # variant. It may include associated information such as quality and phasing. |
| # For example, a call might assign a probability of 0.32 to the occurrence of |
| # a SNP named rs1234 in a call set with the name NA12345. |
| "info": { # A map of additional variant call information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "genotype": [ # The genotype of this variant call. Each value represents either the value |
| # of the `referenceBases` field or a 1-based index into |
| # `alternateBases`. If a variant had a `referenceBases` |
| # value of `T` and an `alternateBases` |
| # value of `["A", "C"]`, and the `genotype` was |
| # `[2, 1]`, that would mean the call |
| # represented the heterozygous value `CA` for this variant. |
| # If the `genotype` was instead `[0, 1]`, the |
| # represented value would be `TA`. Ordering of the |
| # genotype values is important if the `phaseset` is present. |
| # If a genotype is not called (that is, a `.` is present in the |
| # GT string) -1 is returned. |
| 42, |
| ], |
| "callSetId": "A String", # The ID of the call set this variant call belongs to. |
| "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies |
| # the phase of the bases and is consistent with any other variant calls in |
| # the same reference sequence which have the same phaseset value. |
| # When importing data from VCF, if the genotype data was phased but no |
| # phase set was specified this field will be set to `*`. |
| "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry |
| # represents how likely a specific genotype is for this call. The value |
| # ordering is defined by the GL tag in the VCF spec. |
| # If Phred-scaled genotype likelihood scores (PL) are available and |
| # log10(P) genotype likelihood scores (GL) are not, PL scores are converted |
| # to GL scores. If both are available, PL scores are stored in `info`. |
| 3.14, |
| ], |
| "callSetName": "A String", # The name of the call set this variant call belongs to. |
| }, |
| ], |
| "created": "A String", # The date this variant was created, in milliseconds from the epoch. |
| "id": "A String", # The server-generated variant ID, unique across all variants. |
| "filter": [ # A list of filters (normally quality filters) this variant has failed. |
| # `PASS` indicates this variant has passed all filters. |
| "A String", |
| ], |
| "start": "A String", # The position at which this variant occurs (0-based). |
| # This corresponds to the first base of the string of reference bases. |
| "names": [ # Names for the variant, for example a RefSNP ID. |
| "A String", |
| ], |
| "alternateBases": [ # The bases that appear instead of the reference bases. |
| "A String", |
| ], |
| "referenceName": "A String", # The reference on which this variant occurs. |
| # (such as `chr20` or `X`) |
| "quality": 3.14, # A measure of how likely this variant is to be real. |
| # A higher value is better. |
| "referenceBases": "A String", # The reference bases for this variant. They start at the given |
| # position. |
| }, |
| ], |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="search_next">search_next(previous_request, previous_response)</code> |
| <pre>Retrieves the next page of results. |
| |
| Args: |
| previous_request: The request for the previous page. (required) |
| previous_response: The response from the request for the previous page. (required) |
| |
| Returns: |
| A request object that you can call 'execute()' on to request the next |
| page. Returns None if there are no more items in the collection. |
| </pre> |
| </div> |
| |
| </body></html> |
