diff --git a/docs/query-types/variantRequestParameters.md b/docs/query-types/variantRequestParameters.md index 7c0769e..940086e 100644 --- a/docs/query-types/variantRequestParameters.md +++ b/docs/query-types/variantRequestParameters.md @@ -5,15 +5,18 @@ The parameters currently implemented can be looked up in the Beacon v2 default model'e [`genomicVariations/requestParameters`](https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml). + Quoted text below reflects the v2 definitions, some of which might be subject + toc change (e.g. as result of the scouts' process). + ## Beacon v2 Variant Request Parameters ### `assemblyId` In the original Beacon v2 specification `assemblyId` parameter refers to the - genomic assembly accession and version as RefSqeq assembly accession (e.g. "GCF_000001405.39") - or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. "hg38") - or Genome Reference Consortium Human (e.g. GRCh38.p13") names. +> genomic assembly accession and version as RefSqeq assembly accession (e.g. "GCF_000001405.39") +> or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. "hg38") +> or Genome Reference Consortium Human (e.g. GRCh38.p13") names. #### Scouts TODO @@ -27,17 +30,17 @@ In the original Beacon v2 specification `assemblyId` parameter refers to the The `referenceName` parameter matches the - sequence id for genomic sequence (e.g. chromosome) in which variant coordinates - (`start`, `end` ...) are given. Preferably a RefSeqId or alternatively common - synonymus or aliases. +> sequence id for genomic sequence (e.g. chromosome) in which variant coordinates +> (`start`, `end` ...) are given. Preferably a RefSeqId or alternatively common +> synonymus or aliases. #### Examples - - "refseq:NC_000009.12" - - NC_000009.12 - - Chr9 - - "9" - - NC_012920.1 +- refseq:NC_000009.12 +- NC_000009.12 +- Chr9 +- 9 +- NC_012920.1 #### Scouts TODO @@ -62,27 +65,27 @@ are many practical cases for translocation/fusion events). Precise or fuzzy start coordinate position(s) for a variation locus (0-based, inclusive). The use depends on the query type: -* `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` +> * `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` #### Scouts TODO @@ -94,17 +97,21 @@ Precise or fuzzy end coordinate position(s) for a variation locus (0-based, incl This is commonly used for variations w/o specified sequence (although e.g. a range and a sequence motif could be combined). +#### Scouts TODO + +* as above + ### `alternateBases` Sequence of bases for this variation (starting from `start`). -* Accepted values: [ACGTN] -* N is a wildcard, that denotes the position of any base and can be used as -a standalone base of any type or within a partially known sequence. As example, -a query of `ANNT` the Ns can take take any form of [ACGT] and will match -`ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth. -* an _empty value_ is used in the case of deletions with the maximally -trimmed, deleted sequence being indicated in `referenceBases` +> * Accepted values: [ACGTN] +> * N is a wildcard, that denotes the position of any base and can be used as +> a standalone base of any type or within a partially known sequence. As example, +> a query of `ANNT` the Ns can take take any form of [ACGT] and will match +> `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth. +> * an _empty value_ is used in the case of deletions with the maximally +> trimmed, deleted sequence being indicated in `referenceBases` #### Scouts TODO @@ -131,18 +138,20 @@ query type using non-sequence parameters (e.g. `aminoacidChange`). The Beacon v2 schema uses some "VCF-like" examples w/o being prescriptive: - 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` - * BND: breakend, i.e. termination of the allele at position `start` or in - the `startMin` => `startMax` interval, or fusion of the sequence to distant - partner - Either `alternateBases` or `variantType` is required, with the exception - of range queries (single `start` and `end` parameters). +> 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` +> * BND: breakend, i.e. termination of the allele at position `start` or in +> the `startMin` => `startMax` interval, or fusion of the sequence to distant +> partner +> +> Either `alternateBases` or `variantType` is required, with the exception +> of range queries (single `start` and `end` parameters). #### Scouts TODO @@ -160,7 +169,7 @@ The Beacon v2 schema uses some "VCF-like" examples w/o being prescriptive: that length based queries should also be supported for variants with indicated eferenceBases and alternateBases, to enable length-specific wildcard queries. - #### Scouts TODO +#### Scouts TODO * check definition diff --git a/mkdocs.yml b/mkdocs.yml index f70b0f2..982d33f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,7 +12,7 @@ schemas_path: /blob/main/schemas/ nav: - 'Home': / - Variation Types: variant-types - - Request PArameters: query-types/variantRequestParameters + - Request Parameters: query-types/variantRequestParameters - Query Types: query-types - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas