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name: mk-docs | ||
on: | ||
push: | ||
branches: | ||
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permissions: | ||
contents: write | ||
jobs: | ||
deploy: | ||
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with: | ||
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- run: pip install mkdocs-macros-plugin | ||
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- run: pip install mkdocs-mermaid2-plugin | ||
- run: pip install mdx_gh_links | ||
- run: pip install mkdocs-with-pdf | ||
- run: mkdocs gh-deploy --force |
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# variant-query-types | ||
Schemas for genomic / molecular variation queries over the Beacon protocol and beyond |
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:root { | ||
--md-accent-fg-color: #076d63; | ||
} | ||
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.md-grid { | ||
max-width: 1200px; | ||
} | ||
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.md-header__source { | ||
background-image: url("/img/elixir-white-48x36.png"); | ||
background-repeat: no-repeat; | ||
background-position: right; | ||
} | ||
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div.figcaption { | ||
text-align: justify; | ||
line-height: 1.2em; | ||
font-size: 0.8em; | ||
margin: 0 30px 18px 30px; | ||
} | ||
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.md-typeset h1 { | ||
line-height: 1.2em; | ||
margin: 0 0 24px 0; | ||
} | ||
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.md-typeset ul li { | ||
line-height: 1.4em; | ||
margin-bottom: 0.2em; | ||
} | ||
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h2 { | ||
color: var(--md-accent-fg-color); | ||
border-top: var(--md-accent-fg-color) thin solid; | ||
border-bottom: var(--md-accent-fg-color) thin solid; | ||
} | ||
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div.tabbed-set { | ||
background-color: #fafafa; | ||
} | ||
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.tabbed-content { | ||
padding: 5px; | ||
} | ||
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li li { | ||
list-style-type: circle; | ||
} | ||
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li li li { | ||
list-style-type: "–"; | ||
font-size: 0.9em; | ||
} | ||
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.mermaid { | ||
display: flex; | ||
justify-content: center; | ||
} |
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# `VariantBracketRequest` (Beacon v2 default model) | ||
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## Description | ||
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_Bracket Queries_ allow the specification of sequence ranges for both start and end | ||
positions of a genomic variation. The typical example here is the query for similar | ||
structural variants - particularly CNVs - affecting a genomic region but potentially | ||
differing in their exact base extents. | ||
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![Beacon Bracket Query Schema](../img/BeaconBracketQuery-limited-match-graphics.png) | ||
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## Parameters | ||
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* `referenceName` | ||
* `start` (min) and `start` (max) - i.e. 2 start parameters | ||
* `end` (min) and `end` (max) - i.e. 2 end parameters | ||
* `variantType` (optional) | ||
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!!! Warning "Use of `start` and `end`" | ||
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Bracket queries require the use of **two** `start` and `end` parameters, in contrast | ||
to _Range Queries_. | ||
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!!! Attention "List Parameters in GET Requests" | ||
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Since the direct interpretation of list parameters in queries is not supported by | ||
some server environments (e.g. PHP, GO…), list parameters such as `start` and `end` | ||
should be provided as **comma-concatenated** strings when using them in GET requests. | ||
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## Examples | ||
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### CNV Query - _TP53_ Deletion Query by Coordinates | ||
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The following example shows a "bracket query" for focal deletions of the _TP53_ gene locus: | ||
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* The start of the deletion has to occurr anywhere from approx. 2.5Mb 5' of the CDR start to just before the end of the CDR. | ||
* The end of the matched CNVs has to be anywhere from the start of the gene locus to approx. 2.5Mb 3' of its end. | ||
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This leads to matching of deletion CNVs which have at least some base overlap with the gene locus but are not | ||
larger than approx. 5Mb (operational definitions of focality vary between 1 and 5Mb). | ||
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=== "Beacon v2 GET" | ||
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``` | ||
?datasetIds=TEST&referenceName=NC_000017.11&variantType=DEL&start=5000000,7676592&end=7669607,10000000 | ||
``` | ||
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#### Optional | ||
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* `datasetIds=__some-dataset-ids__` | ||
* `filters` ... | ||
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=== "Beacon v2 POST" | ||
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```json | ||
{ | ||
"$schema":"https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json", | ||
"meta": { | ||
"apiVersion": "2.0", | ||
"requestedSchemas": [ | ||
{ | ||
"entityType": "genomicVariation", | ||
"schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json" | ||
} | ||
] | ||
}, | ||
"query": { | ||
"requestParameters": { | ||
"g_variant": { | ||
"referenceName": "NC_000017.11", | ||
"start": [ 5000000, 7676592 ], | ||
"end": [ 7669607, 10000000 ], | ||
"variantType": "DEL" | ||
} | ||
} | ||
}, | ||
"requestedGranularity": "record", | ||
"pagination": { | ||
"skip": 0, | ||
"limit": 5 | ||
} | ||
} | ||
``` | ||
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There are optional parameters [`datasetIds`, `filters` ...] and also the option to specify the response type | ||
(through `requestedGranularity`) and returned data format (`requestedSchemas`). Please follow this up in the | ||
[framework documentation](framework.md). | ||
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=== "Beacon v1" | ||
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``` | ||
?assemblyId=GRCh38&referenceName=17&variantType=DEL&start=5000000,7676592&end=7669607,10000000 | ||
``` | ||
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#### Optional | ||
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* `datasetIds=__some-dataset-ids__` | ||
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=== "Beacon v0.3" | ||
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CNV query options were only implemented with Beacon v0.4, based on Beacon<sup>+</sup> prototyping. | ||
|
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# `VariantRangeRequest` (Beacon v2 default model) | ||
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## Description | ||
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Beacon _Range Queries_ are supposed to return matches of any variant with at least | ||
partial overlap of the sequence range specified by `reference_name`, `start` and `end` | ||
parameters. | ||
|
||
![Beacon Range Query Schema](../img/BeaconRangeQuery-graphics.png) | ||
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## Parameters | ||
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* `referenceName` | ||
* `start` (**single** value) | ||
* `end` (**single** value) | ||
* optional | ||
- `variantType` **OR** `alternateBases` **OR** `aminoacidChange` | ||
- `variantMinLength` | ||
- `variantMaxLength` | ||
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!!! Warning "Use of `start` and `end`" | ||
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Range queries require the use of **single** `start` and `end` parameters, in contrast | ||
to _Bracket Queries_. | ||
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## Examples | ||
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### Any variant affecting _EIF4A1_ | ||
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=== "Beacon v2 GET" | ||
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_RefseqId `referenceName` (recommended)_ | ||
``` | ||
?referenceName=refseq:NC_000017.11&start=7572837&end=7578641 | ||
``` | ||
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_Chromosome style `referenceName` (legacy)_ | ||
``` | ||
?assemblyId=GRCh38&referenceName=17&start=7572837&end=7578641 | ||
``` | ||
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=== "Beacon v2 POST" | ||
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``` | ||
{ | ||
"$schema":"https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json", | ||
"meta": { | ||
"apiVersion": "2.0", | ||
"requestedSchemas": [ | ||
{ | ||
"entityType": "genomicVariation", | ||
"schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json" | ||
} | ||
] | ||
}, | ||
"query": { | ||
"requestParameters": { | ||
"g_variant": | ||
"referenceName": "NC_000017.11", | ||
"start": [ 7572837 ], | ||
"end": [ 7578641 ] | ||
} | ||
} | ||
}, | ||
"requestedGranularity": "record", | ||
"pagination": { | ||
"skip": 0, | ||
"limit": 5 | ||
} | ||
} | ||
``` | ||
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=== "Beacon v1" | ||
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Range Queries are new to Beacon v2 | ||
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||
=== "Beacon v0.3" | ||
|
||
Range Queries are new to Beacon v2 | ||
|
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