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Document operational variant short form style? #158

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mbaudis opened this issue Aug 2, 2024 · 0 comments
Open

Document operational variant short form style? #158

mbaudis opened this issue Aug 2, 2024 · 0 comments
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documentation Improvements or additions to documentation help wanted Extra attention is needed question Further information is requested Variants scout

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@mbaudis
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mbaudis commented Aug 2, 2024

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>AA or 17:123457:>A; and 17:123456:AA>A or 17:123457: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".

@mbaudis mbaudis added documentation Improvements or additions to documentation help wanted Extra attention is needed Variants scout labels Aug 2, 2024
@mbaudis mbaudis changed the title Document operational variant short form style Document operational variant short form style? Aug 2, 2024
@mbaudis mbaudis added the question Further information is requested label Aug 2, 2024
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Labels
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