variant normalization text

Update genomic-coordinates-mappings.md
ga4gh-beacon · Mar 19, 2024 · 4a0fe4f · 4a0fe4f
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diff --git 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 prescribe 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
@@ -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==
diff --git 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==
diff --git 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 → mkdocs.yaml b/mkdocs.yml → 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:
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     - search.highlight