Start on beacon documentation

docs/beacon_doc.md

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+## Variant types
+
+- Supported and existing in our current Beacon: `INS, DEL, SNP`
+
+- Available from the datasets (although not used by the beacon):
+    - in the SweGen dataset: `insertion, SNV, deletion, indel, sequence_alteration`
+    - in the ACpop dataset: `insertion, SNV, deletion`
+
+- What we don't have: `MNP, DUP, BND, INV, CNV, DUP:TANDEM, DEL:ME, INS:ME`
+
+- What we don't know:
+  - How do `indel` and `sequence_alteration` relate to the Beacon variant types? Do they require multiple tags (eg `indel => del + ins`)?
+     `rs200774489` is annotated as `sequence_alteration`, but is an insertion according to https://www.ncbi.nlm.nih.gov/snp/rs200774489
+  - How to communicate which types the datasets support?
+
+
+## Alternate bases
+
+- Allowed: `(ATCGN)+`. Extra value in our data: `*`.
+
+    Should probably be expressed with `N` in the response (`*` is not allowed).
+     - Example, as given in the Beacon response now:
+       ```"referenceName": "22",
+          "start": "16060517",
+          "referenceBases": "T",
+          "alternateBases": "*",
+          "variantType": "SNP"
+       ```
+     In the VCF, this variation is not annotated with `rsid` or `variantType` in the CSQ field.
+
+     From the VCF spec:
+     > The ‘*’ allele is reserved to indicate that the allele is missing due to an overlapping deletion.
+
+     Should rather be shown as (?):
+     ```"referenceName": "22",
+        "start": "16060517",
+        "referenceBases": "T",
+        "alternateBases": "N",
+        "variantType": "DEL"
+     ```