1 <html><body> 2 <style> 3 4 body, h1, h2, h3, div, span, p, pre, a { 5 margin: 0; 6 padding: 0; 7 border: 0; 8 font-weight: inherit; 9 font-style: inherit; 10 font-size: 100%; 11 font-family: inherit; 12 vertical-align: baseline; 13 } 14 15 body { 16 font-size: 13px; 17 padding: 1em; 18 } 19 20 h1 { 21 font-size: 26px; 22 margin-bottom: 1em; 23 } 24 25 h2 { 26 font-size: 24px; 27 margin-bottom: 1em; 28 } 29 30 h3 { 31 font-size: 20px; 32 margin-bottom: 1em; 33 margin-top: 1em; 34 } 35 36 pre, code { 37 line-height: 1.5; 38 font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace; 39 } 40 41 pre { 42 margin-top: 0.5em; 43 } 44 45 h1, h2, h3, p { 46 font-family: Arial, sans serif; 47 } 48 49 h1, h2, h3 { 50 border-bottom: solid #CCC 1px; 51 } 52 53 .toc_element { 54 margin-top: 0.5em; 55 } 56 57 .firstline { 58 margin-left: 2 em; 59 } 60 61 .method { 62 margin-top: 1em; 63 border: solid 1px #CCC; 64 padding: 1em; 65 background: #EEE; 66 } 67 68 .details { 69 font-weight: bold; 70 font-size: 14px; 71 } 72 73 </style> 74 75 <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variants.html">variants</a></h1> 76 <h2>Instance Methods</h2> 77 <p class="toc_element"> 78 <code><a href="#create">create(body, x__xgafv=None)</a></code></p> 79 <p class="firstline">Creates a new variant.</p> 80 <p class="toc_element"> 81 <code><a href="#delete">delete(variantId, x__xgafv=None)</a></code></p> 82 <p class="firstline">Deletes a variant.</p> 83 <p class="toc_element"> 84 <code><a href="#get">get(variantId, x__xgafv=None)</a></code></p> 85 <p class="firstline">Gets a variant by ID.</p> 86 <p class="toc_element"> 87 <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p> 88 <p class="firstline">Creates variant data by asynchronously importing the provided information.</p> 89 <p class="toc_element"> 90 <code><a href="#merge">merge(body, x__xgafv=None)</a></code></p> 91 <p class="firstline">Merges the given variants with existing variants.</p> 92 <p class="toc_element"> 93 <code><a href="#patch">patch(variantId, body, x__xgafv=None, updateMask=None)</a></code></p> 94 <p class="firstline">Updates a variant.</p> 95 <p class="toc_element"> 96 <code><a href="#search">search(body, x__xgafv=None)</a></code></p> 97 <p class="firstline">Gets a list of variants matching the criteria.</p> 98 <p class="toc_element"> 99 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> 100 <p class="firstline">Retrieves the next page of results.</p> 101 <h3>Method Details</h3> 102 <div class="method"> 103 <code class="details" id="create">create(body, x__xgafv=None)</code> 104 <pre>Creates a new variant. 105 106 For the definitions of variants and other genomics resources, see 107 [Fundamentals of Google 108 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 109 110 Args: 111 body: object, The request body. (required) 112 The object takes the form of: 113 114 { # A variant represents a change in DNA sequence relative to a reference 115 # sequence. For example, a variant could represent a SNP or an insertion. 116 # Variants belong to a variant set. 117 # 118 # For more genomics resource definitions, see [Fundamentals of Google 119 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 120 # 121 # Each of the calls on a variant represent a determination of genotype with 122 # respect to that variant. For example, a call might assign probability of 0.32 123 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 124 # belongs to a call set, which contains related calls typically from one 125 # sample. 126 "info": { # A map of additional variant information. This must be of the form 127 # map<string, string[]> (string key mapping to a list of string values). 128 "a_key": [ 129 "", 130 ], 131 }, 132 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 133 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 134 # base after the last base in the reference allele. So, the length of 135 # the reference allele is (end - start). This is useful for variants 136 # that don't explicitly give alternate bases, for example large deletions. 137 "calls": [ # The variant calls for this particular variant. Each one represents the 138 # determination of genotype with respect to this variant. 139 { # A call represents the determination of genotype with respect to a particular 140 # variant. It may include associated information such as quality and phasing. 141 # For example, a call might assign a probability of 0.32 to the occurrence of 142 # a SNP named rs1234 in a call set with the name NA12345. 143 "info": { # A map of additional variant call information. This must be of the form 144 # map<string, string[]> (string key mapping to a list of string values). 145 "a_key": [ 146 "", 147 ], 148 }, 149 "genotype": [ # The genotype of this variant call. Each value represents either the value 150 # of the `referenceBases` field or a 1-based index into 151 # `alternateBases`. If a variant had a `referenceBases` 152 # value of `T` and an `alternateBases` 153 # value of `["A", "C"]`, and the `genotype` was 154 # `[2, 1]`, that would mean the call 155 # represented the heterozygous value `CA` for this variant. 156 # If the `genotype` was instead `[0, 1]`, the 157 # represented value would be `TA`. Ordering of the 158 # genotype values is important if the `phaseset` is present. 159 # If a genotype is not called (that is, a `.` is present in the 160 # GT string) -1 is returned. 161 42, 162 ], 163 "callSetId": "A String", # The ID of the call set this variant call belongs to. 164 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 165 # the phase of the bases and is consistent with any other variant calls in 166 # the same reference sequence which have the same phaseset value. 167 # When importing data from VCF, if the genotype data was phased but no 168 # phase set was specified this field will be set to `*`. 169 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 170 # represents how likely a specific genotype is for this call. The value 171 # ordering is defined by the GL tag in the VCF spec. 172 # If Phred-scaled genotype likelihood scores (PL) are available and 173 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 174 # to GL scores. If both are available, PL scores are stored in `info`. 175 3.14, 176 ], 177 "callSetName": "A String", # The name of the call set this variant call belongs to. 178 }, 179 ], 180 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 181 "id": "A String", # The server-generated variant ID, unique across all variants. 182 "filter": [ # A list of filters (normally quality filters) this variant has failed. 183 # `PASS` indicates this variant has passed all filters. 184 "A String", 185 ], 186 "start": "A String", # The position at which this variant occurs (0-based). 187 # This corresponds to the first base of the string of reference bases. 188 "names": [ # Names for the variant, for example a RefSNP ID. 189 "A String", 190 ], 191 "alternateBases": [ # The bases that appear instead of the reference bases. 192 "A String", 193 ], 194 "referenceName": "A String", # The reference on which this variant occurs. 195 # (such as `chr20` or `X`) 196 "quality": 3.14, # A measure of how likely this variant is to be real. 197 # A higher value is better. 198 "referenceBases": "A String", # The reference bases for this variant. They start at the given 199 # position. 200 } 201 202 x__xgafv: string, V1 error format. 203 Allowed values 204 1 - v1 error format 205 2 - v2 error format 206 207 Returns: 208 An object of the form: 209 210 { # A variant represents a change in DNA sequence relative to a reference 211 # sequence. For example, a variant could represent a SNP or an insertion. 212 # Variants belong to a variant set. 213 # 214 # For more genomics resource definitions, see [Fundamentals of Google 215 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 216 # 217 # Each of the calls on a variant represent a determination of genotype with 218 # respect to that variant. For example, a call might assign probability of 0.32 219 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 220 # belongs to a call set, which contains related calls typically from one 221 # sample. 222 "info": { # A map of additional variant information. This must be of the form 223 # map<string, string[]> (string key mapping to a list of string values). 224 "a_key": [ 225 "", 226 ], 227 }, 228 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 229 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 230 # base after the last base in the reference allele. So, the length of 231 # the reference allele is (end - start). This is useful for variants 232 # that don't explicitly give alternate bases, for example large deletions. 233 "calls": [ # The variant calls for this particular variant. Each one represents the 234 # determination of genotype with respect to this variant. 235 { # A call represents the determination of genotype with respect to a particular 236 # variant. It may include associated information such as quality and phasing. 237 # For example, a call might assign a probability of 0.32 to the occurrence of 238 # a SNP named rs1234 in a call set with the name NA12345. 239 "info": { # A map of additional variant call information. This must be of the form 240 # map<string, string[]> (string key mapping to a list of string values). 241 "a_key": [ 242 "", 243 ], 244 }, 245 "genotype": [ # The genotype of this variant call. Each value represents either the value 246 # of the `referenceBases` field or a 1-based index into 247 # `alternateBases`. If a variant had a `referenceBases` 248 # value of `T` and an `alternateBases` 249 # value of `["A", "C"]`, and the `genotype` was 250 # `[2, 1]`, that would mean the call 251 # represented the heterozygous value `CA` for this variant. 252 # If the `genotype` was instead `[0, 1]`, the 253 # represented value would be `TA`. Ordering of the 254 # genotype values is important if the `phaseset` is present. 255 # If a genotype is not called (that is, a `.` is present in the 256 # GT string) -1 is returned. 257 42, 258 ], 259 "callSetId": "A String", # The ID of the call set this variant call belongs to. 260 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 261 # the phase of the bases and is consistent with any other variant calls in 262 # the same reference sequence which have the same phaseset value. 263 # When importing data from VCF, if the genotype data was phased but no 264 # phase set was specified this field will be set to `*`. 265 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 266 # represents how likely a specific genotype is for this call. The value 267 # ordering is defined by the GL tag in the VCF spec. 268 # If Phred-scaled genotype likelihood scores (PL) are available and 269 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 270 # to GL scores. If both are available, PL scores are stored in `info`. 271 3.14, 272 ], 273 "callSetName": "A String", # The name of the call set this variant call belongs to. 274 }, 275 ], 276 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 277 "id": "A String", # The server-generated variant ID, unique across all variants. 278 "filter": [ # A list of filters (normally quality filters) this variant has failed. 279 # `PASS` indicates this variant has passed all filters. 280 "A String", 281 ], 282 "start": "A String", # The position at which this variant occurs (0-based). 283 # This corresponds to the first base of the string of reference bases. 284 "names": [ # Names for the variant, for example a RefSNP ID. 285 "A String", 286 ], 287 "alternateBases": [ # The bases that appear instead of the reference bases. 288 "A String", 289 ], 290 "referenceName": "A String", # The reference on which this variant occurs. 291 # (such as `chr20` or `X`) 292 "quality": 3.14, # A measure of how likely this variant is to be real. 293 # A higher value is better. 294 "referenceBases": "A String", # The reference bases for this variant. They start at the given 295 # position. 296 }</pre> 297 </div> 298 299 <div class="method"> 300 <code class="details" id="delete">delete(variantId, x__xgafv=None)</code> 301 <pre>Deletes a variant. 302 303 For the definitions of variants and other genomics resources, see 304 [Fundamentals of Google 305 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 306 307 Args: 308 variantId: string, The ID of the variant to be deleted. (required) 309 x__xgafv: string, V1 error format. 310 Allowed values 311 1 - v1 error format 312 2 - v2 error format 313 314 Returns: 315 An object of the form: 316 317 { # A generic empty message that you can re-use to avoid defining duplicated 318 # empty messages in your APIs. A typical example is to use it as the request 319 # or the response type of an API method. For instance: 320 # 321 # service Foo { 322 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); 323 # } 324 # 325 # The JSON representation for `Empty` is empty JSON object `{}`. 326 }</pre> 327 </div> 328 329 <div class="method"> 330 <code class="details" id="get">get(variantId, x__xgafv=None)</code> 331 <pre>Gets a variant by ID. 332 333 For the definitions of variants and other genomics resources, see 334 [Fundamentals of Google 335 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 336 337 Args: 338 variantId: string, The ID of the variant. (required) 339 x__xgafv: string, V1 error format. 340 Allowed values 341 1 - v1 error format 342 2 - v2 error format 343 344 Returns: 345 An object of the form: 346 347 { # A variant represents a change in DNA sequence relative to a reference 348 # sequence. For example, a variant could represent a SNP or an insertion. 349 # Variants belong to a variant set. 350 # 351 # For more genomics resource definitions, see [Fundamentals of Google 352 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 353 # 354 # Each of the calls on a variant represent a determination of genotype with 355 # respect to that variant. For example, a call might assign probability of 0.32 356 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 357 # belongs to a call set, which contains related calls typically from one 358 # sample. 359 "info": { # A map of additional variant information. This must be of the form 360 # map<string, string[]> (string key mapping to a list of string values). 361 "a_key": [ 362 "", 363 ], 364 }, 365 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 366 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 367 # base after the last base in the reference allele. So, the length of 368 # the reference allele is (end - start). This is useful for variants 369 # that don't explicitly give alternate bases, for example large deletions. 370 "calls": [ # The variant calls for this particular variant. Each one represents the 371 # determination of genotype with respect to this variant. 372 { # A call represents the determination of genotype with respect to a particular 373 # variant. It may include associated information such as quality and phasing. 374 # For example, a call might assign a probability of 0.32 to the occurrence of 375 # a SNP named rs1234 in a call set with the name NA12345. 376 "info": { # A map of additional variant call information. This must be of the form 377 # map<string, string[]> (string key mapping to a list of string values). 378 "a_key": [ 379 "", 380 ], 381 }, 382 "genotype": [ # The genotype of this variant call. Each value represents either the value 383 # of the `referenceBases` field or a 1-based index into 384 # `alternateBases`. If a variant had a `referenceBases` 385 # value of `T` and an `alternateBases` 386 # value of `["A", "C"]`, and the `genotype` was 387 # `[2, 1]`, that would mean the call 388 # represented the heterozygous value `CA` for this variant. 389 # If the `genotype` was instead `[0, 1]`, the 390 # represented value would be `TA`. Ordering of the 391 # genotype values is important if the `phaseset` is present. 392 # If a genotype is not called (that is, a `.` is present in the 393 # GT string) -1 is returned. 394 42, 395 ], 396 "callSetId": "A String", # The ID of the call set this variant call belongs to. 397 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 398 # the phase of the bases and is consistent with any other variant calls in 399 # the same reference sequence which have the same phaseset value. 400 # When importing data from VCF, if the genotype data was phased but no 401 # phase set was specified this field will be set to `*`. 402 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 403 # represents how likely a specific genotype is for this call. The value 404 # ordering is defined by the GL tag in the VCF spec. 405 # If Phred-scaled genotype likelihood scores (PL) are available and 406 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 407 # to GL scores. If both are available, PL scores are stored in `info`. 408 3.14, 409 ], 410 "callSetName": "A String", # The name of the call set this variant call belongs to. 411 }, 412 ], 413 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 414 "id": "A String", # The server-generated variant ID, unique across all variants. 415 "filter": [ # A list of filters (normally quality filters) this variant has failed. 416 # `PASS` indicates this variant has passed all filters. 417 "A String", 418 ], 419 "start": "A String", # The position at which this variant occurs (0-based). 420 # This corresponds to the first base of the string of reference bases. 421 "names": [ # Names for the variant, for example a RefSNP ID. 422 "A String", 423 ], 424 "alternateBases": [ # The bases that appear instead of the reference bases. 425 "A String", 426 ], 427 "referenceName": "A String", # The reference on which this variant occurs. 428 # (such as `chr20` or `X`) 429 "quality": 3.14, # A measure of how likely this variant is to be real. 430 # A higher value is better. 431 "referenceBases": "A String", # The reference bases for this variant. They start at the given 432 # position. 433 }</pre> 434 </div> 435 436 <div class="method"> 437 <code class="details" id="import_">import_(body, x__xgafv=None)</code> 438 <pre>Creates variant data by asynchronously importing the provided information. 439 440 For the definitions of variant sets and other genomics resources, see 441 [Fundamentals of Google 442 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 443 444 The variants for import will be merged with any existing variant that 445 matches its reference sequence, start, end, reference bases, and 446 alternative bases. If no such variant exists, a new one will be created. 447 448 When variants are merged, the call information from the new variant 449 is added to the existing variant, and Variant info fields are merged 450 as specified in 451 infoMergeConfig. 452 As a special case, for single-sample VCF files, QUAL and FILTER fields will 453 be moved to the call level; these are sometimes interpreted in a 454 call-specific context. 455 Imported VCF headers are appended to the metadata already in a variant set. 456 457 Args: 458 body: object, The request body. (required) 459 The object takes the form of: 460 461 { # The variant data import request. 462 "variantSetId": "A String", # Required. The variant set to which variant data should be imported. 463 "format": "A String", # The format of the variant data being imported. If unspecified, defaults to 464 # to `VCF`. 465 "sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can 466 # include wildcards [as described 467 # here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). 468 # Note that recursive wildcards ('**') are not supported. 469 "A String", 470 ], 471 "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to 472 # be performed on them. This is plumbed down to the MergeVariantRequests 473 # generated by the resulting import job. 474 "a_key": "A String", 475 }, 476 "normalizeReferenceNames": True or False, # Convert reference names to the canonical representation. 477 # hg19 haploytypes (those reference names containing "_hap") 478 # are not modified in any way. 479 # All other reference names are modified according to the following rules: 480 # The reference name is capitalized. 481 # The "chr" prefix is dropped for all autosomes and sex chromsomes. 482 # For example "chr17" becomes "17" and "chrX" becomes "X". 483 # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". 484 } 485 486 x__xgafv: string, V1 error format. 487 Allowed values 488 1 - v1 error format 489 2 - v2 error format 490 491 Returns: 492 An object of the form: 493 494 { # This resource represents a long-running operation that is the result of a 495 # network API call. 496 "metadata": { # An OperationMetadata object. This will always be returned with the Operation. 497 "a_key": "", # Properties of the object. Contains field @type with type URL. 498 }, 499 "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. 500 # programming environments, including REST APIs and RPC APIs. It is used by 501 # [gRPC](https://github.com/grpc). The error model is designed to be: 502 # 503 # - Simple to use and understand for most users 504 # - Flexible enough to meet unexpected needs 505 # 506 # # Overview 507 # 508 # The `Status` message contains three pieces of data: error code, error message, 509 # and error details. The error code should be an enum value of 510 # google.rpc.Code, but it may accept additional error codes if needed. The 511 # error message should be a developer-facing English message that helps 512 # developers *understand* and *resolve* the error. If a localized user-facing 513 # error message is needed, put the localized message in the error details or 514 # localize it in the client. The optional error details may contain arbitrary 515 # information about the error. There is a predefined set of error detail types 516 # in the package `google.rpc` that can be used for common error conditions. 517 # 518 # # Language mapping 519 # 520 # The `Status` message is the logical representation of the error model, but it 521 # is not necessarily the actual wire format. When the `Status` message is 522 # exposed in different client libraries and different wire protocols, it can be 523 # mapped differently. For example, it will likely be mapped to some exceptions 524 # in Java, but more likely mapped to some error codes in C. 525 # 526 # # Other uses 527 # 528 # The error model and the `Status` message can be used in a variety of 529 # environments, either with or without APIs, to provide a 530 # consistent developer experience across different environments. 531 # 532 # Example uses of this error model include: 533 # 534 # - Partial errors. If a service needs to return partial errors to the client, 535 # it may embed the `Status` in the normal response to indicate the partial 536 # errors. 537 # 538 # - Workflow errors. A typical workflow has multiple steps. Each step may 539 # have a `Status` message for error reporting. 540 # 541 # - Batch operations. If a client uses batch request and batch response, the 542 # `Status` message should be used directly inside batch response, one for 543 # each error sub-response. 544 # 545 # - Asynchronous operations. If an API call embeds asynchronous operation 546 # results in its response, the status of those operations should be 547 # represented directly using the `Status` message. 548 # 549 # - Logging. If some API errors are stored in logs, the message `Status` could 550 # be used directly after any stripping needed for security/privacy reasons. 551 "message": "A String", # A developer-facing error message, which should be in English. Any 552 # user-facing error message should be localized and sent in the 553 # google.rpc.Status.details field, or localized by the client. 554 "code": 42, # The status code, which should be an enum value of google.rpc.Code. 555 "details": [ # A list of messages that carry the error details. There will be a 556 # common set of message types for APIs to use. 557 { 558 "a_key": "", # Properties of the object. Contains field @type with type URL. 559 }, 560 ], 561 }, 562 "done": True or False, # If the value is `false`, it means the operation is still in progress. 563 # If true, the operation is completed, and either `error` or `response` is 564 # available. 565 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. 566 "a_key": "", # Properties of the object. Contains field @type with type URL. 567 }, 568 "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` 569 }</pre> 570 </div> 571 572 <div class="method"> 573 <code class="details" id="merge">merge(body, x__xgafv=None)</code> 574 <pre>Merges the given variants with existing variants. 575 576 For the definitions of variants and other genomics resources, see 577 [Fundamentals of Google 578 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 579 580 Each variant will be 581 merged with an existing variant that matches its reference sequence, 582 start, end, reference bases, and alternative bases. If no such variant 583 exists, a new one will be created. 584 585 When variants are merged, the call information from the new variant 586 is added to the existing variant. Variant info fields are merged as 587 specified in the 588 infoMergeConfig 589 field of the MergeVariantsRequest. 590 591 Please exercise caution when using this method! It is easy to introduce 592 mistakes in existing variants and difficult to back out of them. For 593 example, 594 suppose you were trying to merge a new variant with an existing one and 595 both 596 variants contain calls that belong to callsets with the same callset ID. 597 598 // Existing variant - irrelevant fields trimmed for clarity 599 { 600 "variantSetId": "10473108253681171589", 601 "referenceName": "1", 602 "start": "10582", 603 "referenceBases": "G", 604 "alternateBases": [ 605 "A" 606 ], 607 "calls": [ 608 { 609 "callSetId": "10473108253681171589-0", 610 "callSetName": "CALLSET0", 611 "genotype": [ 612 0, 613 1 614 ], 615 } 616 ] 617 } 618 619 // New variant with conflicting call information 620 { 621 "variantSetId": "10473108253681171589", 622 "referenceName": "1", 623 "start": "10582", 624 "referenceBases": "G", 625 "alternateBases": [ 626 "A" 627 ], 628 "calls": [ 629 { 630 "callSetId": "10473108253681171589-0", 631 "callSetName": "CALLSET0", 632 "genotype": [ 633 1, 634 1 635 ], 636 } 637 ] 638 } 639 640 The resulting merged variant would overwrite the existing calls with those 641 from the new variant: 642 643 { 644 "variantSetId": "10473108253681171589", 645 "referenceName": "1", 646 "start": "10582", 647 "referenceBases": "G", 648 "alternateBases": [ 649 "A" 650 ], 651 "calls": [ 652 { 653 "callSetId": "10473108253681171589-0", 654 "callSetName": "CALLSET0", 655 "genotype": [ 656 1, 657 1 658 ], 659 } 660 ] 661 } 662 663 This may be the desired outcome, but it is up to the user to determine if 664 if that is indeed the case. 665 666 Args: 667 body: object, The request body. (required) 668 The object takes the form of: 669 670 { 671 "variantSetId": "A String", # The destination variant set. 672 "variants": [ # The variants to be merged with existing variants. 673 { # A variant represents a change in DNA sequence relative to a reference 674 # sequence. For example, a variant could represent a SNP or an insertion. 675 # Variants belong to a variant set. 676 # 677 # For more genomics resource definitions, see [Fundamentals of Google 678 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 679 # 680 # Each of the calls on a variant represent a determination of genotype with 681 # respect to that variant. For example, a call might assign probability of 0.32 682 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 683 # belongs to a call set, which contains related calls typically from one 684 # sample. 685 "info": { # A map of additional variant information. This must be of the form 686 # map<string, string[]> (string key mapping to a list of string values). 687 "a_key": [ 688 "", 689 ], 690 }, 691 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 692 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 693 # base after the last base in the reference allele. So, the length of 694 # the reference allele is (end - start). This is useful for variants 695 # that don't explicitly give alternate bases, for example large deletions. 696 "calls": [ # The variant calls for this particular variant. Each one represents the 697 # determination of genotype with respect to this variant. 698 { # A call represents the determination of genotype with respect to a particular 699 # variant. It may include associated information such as quality and phasing. 700 # For example, a call might assign a probability of 0.32 to the occurrence of 701 # a SNP named rs1234 in a call set with the name NA12345. 702 "info": { # A map of additional variant call information. This must be of the form 703 # map<string, string[]> (string key mapping to a list of string values). 704 "a_key": [ 705 "", 706 ], 707 }, 708 "genotype": [ # The genotype of this variant call. Each value represents either the value 709 # of the `referenceBases` field or a 1-based index into 710 # `alternateBases`. If a variant had a `referenceBases` 711 # value of `T` and an `alternateBases` 712 # value of `["A", "C"]`, and the `genotype` was 713 # `[2, 1]`, that would mean the call 714 # represented the heterozygous value `CA` for this variant. 715 # If the `genotype` was instead `[0, 1]`, the 716 # represented value would be `TA`. Ordering of the 717 # genotype values is important if the `phaseset` is present. 718 # If a genotype is not called (that is, a `.` is present in the 719 # GT string) -1 is returned. 720 42, 721 ], 722 "callSetId": "A String", # The ID of the call set this variant call belongs to. 723 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 724 # the phase of the bases and is consistent with any other variant calls in 725 # the same reference sequence which have the same phaseset value. 726 # When importing data from VCF, if the genotype data was phased but no 727 # phase set was specified this field will be set to `*`. 728 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 729 # represents how likely a specific genotype is for this call. The value 730 # ordering is defined by the GL tag in the VCF spec. 731 # If Phred-scaled genotype likelihood scores (PL) are available and 732 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 733 # to GL scores. If both are available, PL scores are stored in `info`. 734 3.14, 735 ], 736 "callSetName": "A String", # The name of the call set this variant call belongs to. 737 }, 738 ], 739 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 740 "id": "A String", # The server-generated variant ID, unique across all variants. 741 "filter": [ # A list of filters (normally quality filters) this variant has failed. 742 # `PASS` indicates this variant has passed all filters. 743 "A String", 744 ], 745 "start": "A String", # The position at which this variant occurs (0-based). 746 # This corresponds to the first base of the string of reference bases. 747 "names": [ # Names for the variant, for example a RefSNP ID. 748 "A String", 749 ], 750 "alternateBases": [ # The bases that appear instead of the reference bases. 751 "A String", 752 ], 753 "referenceName": "A String", # The reference on which this variant occurs. 754 # (such as `chr20` or `X`) 755 "quality": 3.14, # A measure of how likely this variant is to be real. 756 # A higher value is better. 757 "referenceBases": "A String", # The reference bases for this variant. They start at the given 758 # position. 759 }, 760 ], 761 "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to 762 # be performed on them. 763 "a_key": "A String", 764 }, 765 } 766 767 x__xgafv: string, V1 error format. 768 Allowed values 769 1 - v1 error format 770 2 - v2 error format 771 772 Returns: 773 An object of the form: 774 775 { # A generic empty message that you can re-use to avoid defining duplicated 776 # empty messages in your APIs. A typical example is to use it as the request 777 # or the response type of an API method. For instance: 778 # 779 # service Foo { 780 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); 781 # } 782 # 783 # The JSON representation for `Empty` is empty JSON object `{}`. 784 }</pre> 785 </div> 786 787 <div class="method"> 788 <code class="details" id="patch">patch(variantId, body, x__xgafv=None, updateMask=None)</code> 789 <pre>Updates a variant. 790 791 For the definitions of variants and other genomics resources, see 792 [Fundamentals of Google 793 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 794 795 This method supports patch semantics. Returns the modified variant without 796 its calls. 797 798 Args: 799 variantId: string, The ID of the variant to be updated. (required) 800 body: object, The request body. (required) 801 The object takes the form of: 802 803 { # A variant represents a change in DNA sequence relative to a reference 804 # sequence. For example, a variant could represent a SNP or an insertion. 805 # Variants belong to a variant set. 806 # 807 # For more genomics resource definitions, see [Fundamentals of Google 808 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 809 # 810 # Each of the calls on a variant represent a determination of genotype with 811 # respect to that variant. For example, a call might assign probability of 0.32 812 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 813 # belongs to a call set, which contains related calls typically from one 814 # sample. 815 "info": { # A map of additional variant information. This must be of the form 816 # map<string, string[]> (string key mapping to a list of string values). 817 "a_key": [ 818 "", 819 ], 820 }, 821 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 822 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 823 # base after the last base in the reference allele. So, the length of 824 # the reference allele is (end - start). This is useful for variants 825 # that don't explicitly give alternate bases, for example large deletions. 826 "calls": [ # The variant calls for this particular variant. Each one represents the 827 # determination of genotype with respect to this variant. 828 { # A call represents the determination of genotype with respect to a particular 829 # variant. It may include associated information such as quality and phasing. 830 # For example, a call might assign a probability of 0.32 to the occurrence of 831 # a SNP named rs1234 in a call set with the name NA12345. 832 "info": { # A map of additional variant call information. This must be of the form 833 # map<string, string[]> (string key mapping to a list of string values). 834 "a_key": [ 835 "", 836 ], 837 }, 838 "genotype": [ # The genotype of this variant call. Each value represents either the value 839 # of the `referenceBases` field or a 1-based index into 840 # `alternateBases`. If a variant had a `referenceBases` 841 # value of `T` and an `alternateBases` 842 # value of `["A", "C"]`, and the `genotype` was 843 # `[2, 1]`, that would mean the call 844 # represented the heterozygous value `CA` for this variant. 845 # If the `genotype` was instead `[0, 1]`, the 846 # represented value would be `TA`. Ordering of the 847 # genotype values is important if the `phaseset` is present. 848 # If a genotype is not called (that is, a `.` is present in the 849 # GT string) -1 is returned. 850 42, 851 ], 852 "callSetId": "A String", # The ID of the call set this variant call belongs to. 853 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 854 # the phase of the bases and is consistent with any other variant calls in 855 # the same reference sequence which have the same phaseset value. 856 # When importing data from VCF, if the genotype data was phased but no 857 # phase set was specified this field will be set to `*`. 858 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 859 # represents how likely a specific genotype is for this call. The value 860 # ordering is defined by the GL tag in the VCF spec. 861 # If Phred-scaled genotype likelihood scores (PL) are available and 862 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 863 # to GL scores. If both are available, PL scores are stored in `info`. 864 3.14, 865 ], 866 "callSetName": "A String", # The name of the call set this variant call belongs to. 867 }, 868 ], 869 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 870 "id": "A String", # The server-generated variant ID, unique across all variants. 871 "filter": [ # A list of filters (normally quality filters) this variant has failed. 872 # `PASS` indicates this variant has passed all filters. 873 "A String", 874 ], 875 "start": "A String", # The position at which this variant occurs (0-based). 876 # This corresponds to the first base of the string of reference bases. 877 "names": [ # Names for the variant, for example a RefSNP ID. 878 "A String", 879 ], 880 "alternateBases": [ # The bases that appear instead of the reference bases. 881 "A String", 882 ], 883 "referenceName": "A String", # The reference on which this variant occurs. 884 # (such as `chr20` or `X`) 885 "quality": 3.14, # A measure of how likely this variant is to be real. 886 # A higher value is better. 887 "referenceBases": "A String", # The reference bases for this variant. They start at the given 888 # position. 889 } 890 891 x__xgafv: string, V1 error format. 892 Allowed values 893 1 - v1 error format 894 2 - v2 error format 895 updateMask: string, An optional mask specifying which fields to update. At this time, mutable 896 fields are names and 897 info. Acceptable values are "names" and 898 "info". If unspecified, all mutable fields will be updated. 899 900 Returns: 901 An object of the form: 902 903 { # A variant represents a change in DNA sequence relative to a reference 904 # sequence. For example, a variant could represent a SNP or an insertion. 905 # Variants belong to a variant set. 906 # 907 # For more genomics resource definitions, see [Fundamentals of Google 908 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 909 # 910 # Each of the calls on a variant represent a determination of genotype with 911 # respect to that variant. For example, a call might assign probability of 0.32 912 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 913 # belongs to a call set, which contains related calls typically from one 914 # sample. 915 "info": { # A map of additional variant information. This must be of the form 916 # map<string, string[]> (string key mapping to a list of string values). 917 "a_key": [ 918 "", 919 ], 920 }, 921 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 922 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 923 # base after the last base in the reference allele. So, the length of 924 # the reference allele is (end - start). This is useful for variants 925 # that don't explicitly give alternate bases, for example large deletions. 926 "calls": [ # The variant calls for this particular variant. Each one represents the 927 # determination of genotype with respect to this variant. 928 { # A call represents the determination of genotype with respect to a particular 929 # variant. It may include associated information such as quality and phasing. 930 # For example, a call might assign a probability of 0.32 to the occurrence of 931 # a SNP named rs1234 in a call set with the name NA12345. 932 "info": { # A map of additional variant call information. This must be of the form 933 # map<string, string[]> (string key mapping to a list of string values). 934 "a_key": [ 935 "", 936 ], 937 }, 938 "genotype": [ # The genotype of this variant call. Each value represents either the value 939 # of the `referenceBases` field or a 1-based index into 940 # `alternateBases`. If a variant had a `referenceBases` 941 # value of `T` and an `alternateBases` 942 # value of `["A", "C"]`, and the `genotype` was 943 # `[2, 1]`, that would mean the call 944 # represented the heterozygous value `CA` for this variant. 945 # If the `genotype` was instead `[0, 1]`, the 946 # represented value would be `TA`. Ordering of the 947 # genotype values is important if the `phaseset` is present. 948 # If a genotype is not called (that is, a `.` is present in the 949 # GT string) -1 is returned. 950 42, 951 ], 952 "callSetId": "A String", # The ID of the call set this variant call belongs to. 953 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 954 # the phase of the bases and is consistent with any other variant calls in 955 # the same reference sequence which have the same phaseset value. 956 # When importing data from VCF, if the genotype data was phased but no 957 # phase set was specified this field will be set to `*`. 958 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 959 # represents how likely a specific genotype is for this call. The value 960 # ordering is defined by the GL tag in the VCF spec. 961 # If Phred-scaled genotype likelihood scores (PL) are available and 962 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 963 # to GL scores. If both are available, PL scores are stored in `info`. 964 3.14, 965 ], 966 "callSetName": "A String", # The name of the call set this variant call belongs to. 967 }, 968 ], 969 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 970 "id": "A String", # The server-generated variant ID, unique across all variants. 971 "filter": [ # A list of filters (normally quality filters) this variant has failed. 972 # `PASS` indicates this variant has passed all filters. 973 "A String", 974 ], 975 "start": "A String", # The position at which this variant occurs (0-based). 976 # This corresponds to the first base of the string of reference bases. 977 "names": [ # Names for the variant, for example a RefSNP ID. 978 "A String", 979 ], 980 "alternateBases": [ # The bases that appear instead of the reference bases. 981 "A String", 982 ], 983 "referenceName": "A String", # The reference on which this variant occurs. 984 # (such as `chr20` or `X`) 985 "quality": 3.14, # A measure of how likely this variant is to be real. 986 # A higher value is better. 987 "referenceBases": "A String", # The reference bases for this variant. They start at the given 988 # position. 989 }</pre> 990 </div> 991 992 <div class="method"> 993 <code class="details" id="search">search(body, x__xgafv=None)</code> 994 <pre>Gets a list of variants matching the criteria. 995 996 For the definitions of variants and other genomics resources, see 997 [Fundamentals of Google 998 Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 999 1000 Implements 1001 [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126). 1002 1003 Args: 1004 body: object, The request body. (required) 1005 The object takes the form of: 1006 1007 { # The variant search request. 1008 "end": "A String", # The end of the window, 0-based exclusive. If unspecified or 0, defaults to 1009 # the length of the reference. 1010 "pageSize": 42, # The maximum number of variants to return in a single page. If unspecified, 1011 # defaults to 5000. The maximum value is 10000. 1012 "start": "A String", # The beginning of the window (0-based, inclusive) for which 1013 # overlapping variants should be returned. If unspecified, defaults to 0. 1014 "maxCalls": 42, # The maximum number of calls to return in a single page. Note that this 1015 # limit may be exceeded in the event that a matching variant contains more 1016 # calls than the requested maximum. If unspecified, defaults to 5000. The 1017 # maximum value is 10000. 1018 "pageToken": "A String", # The continuation token, which is used to page through large result sets. 1019 # To get the next page of results, set this parameter to the value of 1020 # `nextPageToken` from the previous response. 1021 "variantSetIds": [ # At most one variant set ID must be provided. Only variants from this 1022 # variant set will be returned. If omitted, a call set id must be included in 1023 # the request. 1024 "A String", 1025 ], 1026 "variantName": "A String", # Only return variants which have exactly this name. 1027 "referenceName": "A String", # Required. Only return variants in this reference sequence. 1028 "callSetIds": [ # Only return variant calls which belong to call sets with these ids. 1029 # Leaving this blank returns all variant calls. If a variant has no 1030 # calls belonging to any of these call sets, it won't be returned at all. 1031 "A String", 1032 ], 1033 } 1034 1035 x__xgafv: string, V1 error format. 1036 Allowed values 1037 1 - v1 error format 1038 2 - v2 error format 1039 1040 Returns: 1041 An object of the form: 1042 1043 { # The variant search response. 1044 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. 1045 # Provide this value in a subsequent request to return the next page of 1046 # results. This field will be empty if there aren't any additional results. 1047 "variants": [ # The list of matching Variants. 1048 { # A variant represents a change in DNA sequence relative to a reference 1049 # sequence. For example, a variant could represent a SNP or an insertion. 1050 # Variants belong to a variant set. 1051 # 1052 # For more genomics resource definitions, see [Fundamentals of Google 1053 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1054 # 1055 # Each of the calls on a variant represent a determination of genotype with 1056 # respect to that variant. For example, a call might assign probability of 0.32 1057 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 1058 # belongs to a call set, which contains related calls typically from one 1059 # sample. 1060 "info": { # A map of additional variant information. This must be of the form 1061 # map<string, string[]> (string key mapping to a list of string values). 1062 "a_key": [ 1063 "", 1064 ], 1065 }, 1066 "variantSetId": "A String", # The ID of the variant set this variant belongs to. 1067 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first 1068 # base after the last base in the reference allele. So, the length of 1069 # the reference allele is (end - start). This is useful for variants 1070 # that don't explicitly give alternate bases, for example large deletions. 1071 "calls": [ # The variant calls for this particular variant. Each one represents the 1072 # determination of genotype with respect to this variant. 1073 { # A call represents the determination of genotype with respect to a particular 1074 # variant. It may include associated information such as quality and phasing. 1075 # For example, a call might assign a probability of 0.32 to the occurrence of 1076 # a SNP named rs1234 in a call set with the name NA12345. 1077 "info": { # A map of additional variant call information. This must be of the form 1078 # map<string, string[]> (string key mapping to a list of string values). 1079 "a_key": [ 1080 "", 1081 ], 1082 }, 1083 "genotype": [ # The genotype of this variant call. Each value represents either the value 1084 # of the `referenceBases` field or a 1-based index into 1085 # `alternateBases`. If a variant had a `referenceBases` 1086 # value of `T` and an `alternateBases` 1087 # value of `["A", "C"]`, and the `genotype` was 1088 # `[2, 1]`, that would mean the call 1089 # represented the heterozygous value `CA` for this variant. 1090 # If the `genotype` was instead `[0, 1]`, the 1091 # represented value would be `TA`. Ordering of the 1092 # genotype values is important if the `phaseset` is present. 1093 # If a genotype is not called (that is, a `.` is present in the 1094 # GT string) -1 is returned. 1095 42, 1096 ], 1097 "callSetId": "A String", # The ID of the call set this variant call belongs to. 1098 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies 1099 # the phase of the bases and is consistent with any other variant calls in 1100 # the same reference sequence which have the same phaseset value. 1101 # When importing data from VCF, if the genotype data was phased but no 1102 # phase set was specified this field will be set to `*`. 1103 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry 1104 # represents how likely a specific genotype is for this call. The value 1105 # ordering is defined by the GL tag in the VCF spec. 1106 # If Phred-scaled genotype likelihood scores (PL) are available and 1107 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted 1108 # to GL scores. If both are available, PL scores are stored in `info`. 1109 3.14, 1110 ], 1111 "callSetName": "A String", # The name of the call set this variant call belongs to. 1112 }, 1113 ], 1114 "created": "A String", # The date this variant was created, in milliseconds from the epoch. 1115 "id": "A String", # The server-generated variant ID, unique across all variants. 1116 "filter": [ # A list of filters (normally quality filters) this variant has failed. 1117 # `PASS` indicates this variant has passed all filters. 1118 "A String", 1119 ], 1120 "start": "A String", # The position at which this variant occurs (0-based). 1121 # This corresponds to the first base of the string of reference bases. 1122 "names": [ # Names for the variant, for example a RefSNP ID. 1123 "A String", 1124 ], 1125 "alternateBases": [ # The bases that appear instead of the reference bases. 1126 "A String", 1127 ], 1128 "referenceName": "A String", # The reference on which this variant occurs. 1129 # (such as `chr20` or `X`) 1130 "quality": 3.14, # A measure of how likely this variant is to be real. 1131 # A higher value is better. 1132 "referenceBases": "A String", # The reference bases for this variant. They start at the given 1133 # position. 1134 }, 1135 ], 1136 }</pre> 1137 </div> 1138 1139 <div class="method"> 1140 <code class="details" id="search_next">search_next(previous_request, previous_response)</code> 1141 <pre>Retrieves the next page of results. 1142 1143 Args: 1144 previous_request: The request for the previous page. (required) 1145 previous_response: The response from the request for the previous page. (required) 1146 1147 Returns: 1148 A request object that you can call 'execute()' on to request the next 1149 page. Returns None if there are no more items in the collection. 1150 </pre> 1151 </div> 1152 1153 </body></html>
