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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 46a8071fe1d1a112dcc791f61c20fd8306b4061f / . / docs / dyn / genomics_v1beta.variants.html
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75<h1><a href="genomics_v1beta.html">Genomics API</a> . <a href="genomics_v1beta.variants.html">variants</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="#create">create(body)</a></code></p>
79<p class="firstline">Creates a new variant.</p>
80<p class="toc_element">
81 <code><a href="#delete">delete(variantId)</a></code></p>
82<p class="firstline">Deletes a variant.</p>
83<p class="toc_element">
84 <code><a href="#export">export(body)</a></code></p>
85<p class="firstline">Exports variant data to an external destination.</p>
86<p class="toc_element">
87 <code><a href="#get">get(variantId)</a></code></p>
88<p class="firstline">Gets a variant by ID.</p>
89<p class="toc_element">
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]90 <code><a href="#import_">import_(body)</a></code></p>
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]91<p class="firstline">Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. 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 VariantSet.</p>
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]92<p class="toc_element">
93 <code><a href="#search">search(body)</a></code></p>
94<p class="firstline">Gets a list of variants matching the criteria.</p>
95<p class="toc_element">
96 <code><a href="#update">update(variantId, body)</a></code></p>
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]97<p class="firstline">Updates a variant's names and info fields. All other modifications are silently ignored. Returns the modified variant without its calls.</p>
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]98<h3>Method Details</h3>
99<div class="method">
100 <code class="details" id="create">create(body)</code>
101 <pre>Creates a new variant.
102
103Args:
104 body: object, The request body. (required)
105 The object takes the form of:
106
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]107{ # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]108 "info": { # A map of additional variant information.
109 "a_key": [ # A string which maps to an array of values.
110 "A String",
111 ],
112 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]113 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
114 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]115 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]116 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]117 "info": { # A map of additional variant call information.
118 "a_key": [ # A string which maps to an array of values.
119 "A String",
120 ],
121 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]122 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]123 42,
124 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]125 "callSetId": "A String", # The ID of the call set this variant call belongs to.
126 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]127 "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.
128 3.14,
129 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]130 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]131 },
132 ],
133 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
134 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]135 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
136 "A String",
137 ],
138 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]139 "names": [ # Names for the variant, for example a RefSNP ID.
140 "A String",
141 ],
142 "alternateBases": [ # The bases that appear instead of the reference bases.
143 "A String",
144 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]145 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
146 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]147 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]148}
149
150
151Returns:
152 An object of the form:
153
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]154 { # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]155 "info": { # A map of additional variant information.
156 "a_key": [ # A string which maps to an array of values.
157 "A String",
158 ],
159 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]160 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
161 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]162 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]163 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]164 "info": { # A map of additional variant call information.
165 "a_key": [ # A string which maps to an array of values.
166 "A String",
167 ],
168 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]169 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]170 42,
171 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]172 "callSetId": "A String", # The ID of the call set this variant call belongs to.
173 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]174 "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.
175 3.14,
176 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]177 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]178 },
179 ],
180 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
181 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]182 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
183 "A String",
184 ],
185 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]186 "names": [ # Names for the variant, for example a RefSNP ID.
187 "A String",
188 ],
189 "alternateBases": [ # The bases that appear instead of the reference bases.
190 "A String",
191 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]192 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
193 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]194 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]195 }</pre>
196</div>
197
198<div class="method">
199 <code class="details" id="delete">delete(variantId)</code>
200 <pre>Deletes a variant.
201
202Args:
203 variantId: string, The ID of the variant to be deleted. (required)
204</pre>
205</div>
206
207<div class="method">
208 <code class="details" id="export">export(body)</code>
209 <pre>Exports variant data to an external destination.
210
211Args:
212 body: object, The request body. (required)
213 The object takes the form of:
214
215{ # The variant data export request.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]216 "variantSetId": "A String", # Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]217 "format": "A String", # The format for the exported data.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]218 "projectId": "A String", # The Google Cloud project number that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.
219 "callSetIds": [ # If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]220 "A String",
221 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]222 "bigqueryDataset": "A String", # The BigQuery dataset to export data to. Note that this is distinct from the Genomics concept of "dataset".
223 "bigqueryTable": "A String", # The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]224 }
225
226
227Returns:
228 An object of the form:
229
230 { # The variant data export response.
231 "jobId": "A String", # A job ID that can be used to get status information.
232 }</pre>
233</div>
234
235<div class="method">
236 <code class="details" id="get">get(variantId)</code>
237 <pre>Gets a variant by ID.
238
239Args:
240 variantId: string, The ID of the variant. (required)
241
242Returns:
243 An object of the form:
244
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]245 { # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]246 "info": { # A map of additional variant information.
247 "a_key": [ # A string which maps to an array of values.
248 "A String",
249 ],
250 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]251 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
252 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]253 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]254 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]255 "info": { # A map of additional variant call information.
256 "a_key": [ # A string which maps to an array of values.
257 "A String",
258 ],
259 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]260 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]261 42,
262 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]263 "callSetId": "A String", # The ID of the call set this variant call belongs to.
264 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]265 "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.
266 3.14,
267 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]268 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]269 },
270 ],
271 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
272 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]273 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
274 "A String",
275 ],
276 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]277 "names": [ # Names for the variant, for example a RefSNP ID.
278 "A String",
279 ],
280 "alternateBases": [ # The bases that appear instead of the reference bases.
281 "A String",
282 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]283 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
284 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]285 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]286 }</pre>
287</div>
288
289<div class="method">
290 <code class="details" id="import_">import_(body)</code>
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]291 <pre>Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. 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 VariantSet.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]292
293Args:
294 body: object, The request body. (required)
295 The object takes the form of:
296
297{ # The variant data import request.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]298 "variantSetId": "A String", # Required. The variant set to which variant data should be imported.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]299 "sourceUris": [ # A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF Specification for more details on the input format.
300 "A String",
301 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]302 "format": "A String", # The format of the variant data being imported.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]303 }
304
305
306Returns:
307 An object of the form:
308
309 { # The variant data import response.
310 "jobId": "A String", # A job ID that can be used to get status information.
311 }</pre>
312</div>
313
314<div class="method">
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]315 <code class="details" id="search">search(body)</code>
316 <pre>Gets a list of variants matching the criteria.
317
318Args:
319 body: object, The request body. (required)
320 The object takes the form of:
321
322{ # The variant search request.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]323 "end": "A String", # Required. The end of the window (0-based, exclusive) for which overlapping variants should be returned.
324 "pageSize": 42, # The maximum number of variants to return.
325 "start": "A String", # Required. The beginning of the window (0-based, inclusive) for which overlapping variants should be returned.
326 "maxCalls": 42, # The maximum number of calls to return. However, at least one variant will always be returned, even if it has more calls than this limit.
327 "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.
328 "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. Currently, variants with no calls from any call set will never be returned.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]329 "A String",
330 ],
331 "variantName": "A String", # Only return variants which have exactly this name.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]332 "referenceName": "A String", # Required. Only return variants in this reference sequence.
333 "variantSetIds": [ # Exactly one variant set ID must be provided. Only variants from this variant set will be returned.
334 "A String",
335 ],
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]336 }
337
338
339Returns:
340 An object of the form:
341
342 { # The variant search response.
343 "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.
344 "variants": [ # The list of matching Variants.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]345 { # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]346 "info": { # A map of additional variant information.
347 "a_key": [ # A string which maps to an array of values.
348 "A String",
349 ],
350 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]351 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
352 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]353 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]354 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]355 "info": { # A map of additional variant call information.
356 "a_key": [ # A string which maps to an array of values.
357 "A String",
358 ],
359 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]360 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]361 42,
362 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]363 "callSetId": "A String", # The ID of the call set this variant call belongs to.
364 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]365 "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.
366 3.14,
367 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]368 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]369 },
370 ],
371 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
372 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]373 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
374 "A String",
375 ],
376 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]377 "names": [ # Names for the variant, for example a RefSNP ID.
378 "A String",
379 ],
380 "alternateBases": [ # The bases that appear instead of the reference bases.
381 "A String",
382 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]383 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
384 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]385 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]386 },
387 ],
388 }</pre>
389</div>
390
391<div class="method">
392 <code class="details" id="update">update(variantId, body)</code>
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]393 <pre>Updates a variant's names and info fields. All other modifications are silently ignored. Returns the modified variant without its calls.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]394
395Args:
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]396 variantId: string, The ID of the variant to be updated. (required)
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]397 body: object, The request body. (required)
398 The object takes the form of:
399
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]400{ # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]401 "info": { # A map of additional variant information.
402 "a_key": [ # A string which maps to an array of values.
403 "A String",
404 ],
405 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]406 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
407 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]408 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]409 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]410 "info": { # A map of additional variant call information.
411 "a_key": [ # A string which maps to an array of values.
412 "A String",
413 ],
414 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]415 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]416 42,
417 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]418 "callSetId": "A String", # The ID of the call set this variant call belongs to.
419 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]420 "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.
421 3.14,
422 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]423 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]424 },
425 ],
426 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
427 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]428 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
429 "A String",
430 ],
431 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]432 "names": [ # Names for the variant, for example a RefSNP ID.
433 "A String",
434 ],
435 "alternateBases": [ # The bases that appear instead of the reference bases.
436 "A String",
437 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]438 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
439 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]440 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]441}
442
443
444Returns:
445 An object of the form:
446
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]447 { # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]448 "info": { # A map of additional variant information.
449 "a_key": [ # A string which maps to an array of values.
450 "A String",
451 ],
452 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]453 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
454 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]455 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]456 { # 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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]457 "info": { # A map of additional variant call information.
458 "a_key": [ # A string which maps to an array of values.
459 "A String",
460 ],
461 },
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]462 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]463 42,
464 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]465 "callSetId": "A String", # The ID of the call set this variant call belongs to.
466 "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 *.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]467 "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.
468 3.14,
469 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]470 "callSetName": "A String", # The name of the call set this variant call belongs to.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]471 },
472 ],
473 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
474 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]475 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
476 "A String",
477 ],
478 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]479 "names": [ # Names for the variant, for example a RefSNP ID.
480 "A String",
481 ],
482 "alternateBases": [ # The bases that appear instead of the reference bases.
483 "A String",
484 ],
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]485 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
486 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]487 "id": "A String", # The Google generated ID of the variant, immutable.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]488 }</pre>
489</div>
490
491</body></html>