diff --git a/docs/genomic-coordinates-mappings.md b/docs/genomic-coordinates-mappings.md index b1d77cd..7f58d92 100644 --- a/docs/genomic-coordinates-mappings.md +++ b/docs/genomic-coordinates-mappings.md @@ -9,7 +9,18 @@ ## Variant normalization -==TBD== +The Beacon v2 specification does not define which style of variant normalization +sequence defined queries are based on. In practice usually the VCF model is assumed +(parsimony with avoidance of empty alleles). However, the GA4GH VRS specification +argues against this practice and recommends a fully justified normalization[^2]. + +!!! bug "Beacon Scouts To Do" + + The Beacon Variant Scouts team will work on documenting a recommended variant + normalization format which might deviate from current practices. + + [^1]: Source: [@andrewyatz](https://github.com/@andrewyatz/) at [GenomeStandards](https://genomestandards.org/standards/genome-coordinates/) +[^2]: VRS normalization rules as design decision: [Alleles are Fully Justified](https://vrs.ga4gh.org/en/latest/appendices/design_decisions.html#alleles-are-fully-justified) diff --git a/docs/query-solutions.md b/docs/query-solutions.md index f944285..ca56922 100644 --- a/docs/query-solutions.md +++ b/docs/query-solutions.md @@ -6,6 +6,11 @@ TODO: * GET vs. POST examples --> +!!! bug "Beacon Scouts To Do" + + Please extend the examples... + + ## Any deletion(s) involving the TP53 gene locus ??? tip "Using `VariantRangeRequest`" @@ -69,4 +74,3 @@ TODO: ?referenceName=refseq:NC_000002.12&start=0,54700000&end=63900000,242193529&variantType=SO:0001742 ``` -==TBD== \ No newline at end of file diff --git a/docs/terms-and-values.md b/docs/terms-and-values.md index cd9deff..af7078e 100644 --- a/docs/terms-and-values.md +++ b/docs/terms-and-values.md @@ -12,4 +12,9 @@ The main examples relevant to variation queries here are `referenceName` and to promote flexibility (e.g. non-human use cases) and simple adoption (e.g. reusing VCF terms). +!!! bug "Beacon Scouts To Do" + + We will add and document recommended termionologies and use case examples during + the _2024 Beacon Variation Scouts_ process. + ==TBD== \ No newline at end of file diff --git a/docs/variant-types.md b/docs/variant-types.md index ad96436..386f9e1 100644 --- a/docs/variant-types.md +++ b/docs/variant-types.md @@ -9,6 +9,12 @@ manifestations. For a start please see the previous [Beacon Scouts: Genomic Variants Use Cases & Examples](https://docs.google.com/document/d/1cwwRQ2PtlN1dBffCugdkbSHWCPmLgLkADd-5mu-rVAw/edit). +!!! bug "Beacon Scouts To Do" + + We will add and document the variation concepts during the 2024 Beacon Variation + Scouts process. + + ## Implemented ### Allelic Sequence Variations diff --git a/mkdocs.yml b/mkdocs.yaml similarity index 95% rename from mkdocs.yml rename to mkdocs.yaml index 4a2a2a8..6ae4749 100644 --- a/mkdocs.yml +++ b/mkdocs.yaml @@ -65,7 +65,9 @@ theme: logo: img/GA-logo.png favicon: img/ga4gh_circle.ico icon: - repo: fontawesome/brands/github-alt + repo: fontawesome/brands/github-alt + admonition: + bug: fontawesome/regular/hourglass-half features: - content.tabs.link - search.highlight