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Variants scoutdocumentationImprovements or additions to documentationImprovements or additions to documentationhelp wantedExtra attention is neededExtra attention is neededquestionFurther information is requestedFurther information is requested
Description
When discussing variant queries or even as part of of UI implementations frequently "short form" annotations are being used instead of parameter=value pairs; but there is no recommended style or parameter specification. One can usually see something like chr17, 123456 A>C the a bit nicer 17:123456:A>C etc.; and this seems fairly understandable (given that the genome edition is indicated somewhere), but:
- this only works as a private shorthand, not for reusable implementations
- the parameters are ambiguous since e.g. it is not defined if the base position is indicated in UI space (1 based) or Beacon API convention (0 based)
- there are ambiguous options when indicating e.g. INDELs - is it
17:123456:A>AAor17:123457:>A; and17:123456:AA>Aor17:123457:A>? (i.e. use of anchor bases - and other issues regarding normalization) - ... and the questions then for more technical re-use of formats for ranges and brackets, variant types, whitespace, separators ... etc.
Question Should we (e.g. through variant scouts) develop a simple schema w/ recommendations of which formats etc. to use? Outside of the specification, but as part of an "ecosystem for recommendations".
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Variants scoutdocumentationImprovements or additions to documentationImprovements or additions to documentationhelp wantedExtra attention is neededExtra attention is neededquestionFurther information is requestedFurther information is requested