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requestParameters.yaml
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requestParameters.yaml
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$schema: https://json-schema.org/draft/2020-12/schema
g_variant:
type: object
properties:
assemblyId:
$ref: ./requestParametersComponents.yaml#/definitions/Assembly
referenceName:
$ref: ./requestParametersComponents.yaml#/definitions/RefSeqId
start:
description: >-
Precise or fuzzy start coordinate position(s), allele locus
(0-based, inclusive).
* `start` only:
- for single positions, e.g. the start of a specified sequence
alteration where the size is given through the specified `alternateBases`
- typical use are queries for SNV and small InDels
- the use of `start` without an `end` parameter requires the use of
`alternateBases`
* `start` and `end`:
- for searching any variant falling fully or partially within the range
between `start` and `end` (a.k.a. "range query")
- additional use of `variantType` OR `alternateBases` can limit the
scope of the query
- by convention, partial overlaps of variants with the indicated genomic
range are accepted; for specific overlap requirements the 4-parameter
"Bracket Queries" should be employed
* 2 values in both `start` and `end` for constructing a "Bracket Query":
- can be used to match any contiguous genomic interval, e.g. for querying
imprecise positions
- identifies all structural variants starting between `start[0]` and `start[1]`,
and ending between `end[0]` <-> `end[1]`
- single or double sided precise matches can be achieved by setting
`start[1]=start[0]+1` and `end[1]=end[0]+1`
type: array
items:
type: integer
format: int64
minimum: 0
minItems: 1
maxItems: 2
end:
description: >-
Precise or bracketing the end of the variants of interest:
* (0-based, exclusive) - see `start`
* for bracket queries, provide 2 values (e.g. [111,222])."
type: array
items:
type: integer
format: int64
minimum: 1
minItems: 0
maxItems: 2
referenceBases:
$ref: ./requestParametersComponents.yaml#/definitions/ReferenceBases
alternateBases:
$ref: ./requestParametersComponents.yaml#/definitions/AlternateBases
variantType:
description: >-
The `variantType` is used to query variants which are not defined through
a sequence of one or more bases using the `alternateBases` parameter.
Examples here are e.g. structural variants:
* DUP
- increased allelic count of material from the genomic region between
`start` and `end` positions
- no assumption about the placement of the additional sequences is being
made (i.e. no _in situ_ requirement as tandem duplications)
* DEL: deletion of sequence following `start`
The Beacon model is not prescriptive with regard to the values allowed
for `variantType` with use of extended types (such as from `EFO:0030063`)
being permitted. However, a support for the basic CNV types above - where
represented in the data - is recommended.
type: string
examples:
- EFO:0030070
- DUP
- DEL
- EFO:0030069
variantMinLength:
description: >-
* Minimum length in bases of a genomic variant
* This is an optional parameter without prescribed use. While a length is
commonly available for structural variants such as copy number variations,
it is recommended that length based queries should also be supported for
variants with indicated referenceBases and alternateBases, to enable
length-specific wildcard queries.
type: integer
format: int64
minimum: 0
variantMaxLength:
description: >-
* Maximum length in bases of a genomic variant.
* This is an optional parameter without prescribed use. While a length is
commonly available for structural variants such as copy number variations,
it is recommended that length based queries should also be supported for
variants with indicated referenceBases and alternateBases, to enable
length-specific wildcard queries.
type: integer
format: int64
minimum: 1
mateName:
$ref: ./requestParametersComponents.yaml#/definitions/RefSeqId
geneId:
description: >-
* A gene identifier
* It is strongly suggested to use a symbol following
the HGNC (https://www.genenames.org) nomenclature.
type: string
examples:
- BRAF
- SCN5A
aminoacidChange:
description: Aminoacid alteration of interest. Format 1 letter
type: string
examples:
- V600E
- M734V
genomicAlleleShortForm:
description: HGVSId descriptor
type: string
examples:
- NM_004006.2:c.4375C>T