Specifications about start and end

[Diana Lemos]

Hello,

I have a couple of questions about the specifications. Some of them are not very clear about the input options that can be used. 

Questions 1

Is it allowed to input 'start' and 'end' when searching for a SNV? 

In the specifications says: 'start and end: special use case for exactly determined structural changes'. 

Which made me think that for SNV and small indels the input has to be 'start' (without end) and always use 'referenceBases'. However, I saw a few beacons that allow 'start' and 'end' for all types of variants. 

Also, I saw this example:

  variantType: "SNP",

  referenceBases: "C",

  referenceName: "1",

  start: 64628929,

  assemblyId: "GRCh38",

  includeDatasetResponses: "ALL"

in this example 'variantType' is used to represent a SNP but in the specification says 'variantType is used to denote e.g. structural variants'. 

Question 2

For structural variants, the specifications are not really clear if the to input can allow 'start', 'end', 'startMin', 'startMax', 'endMin' and 'endMax' all at the same time. 

I was thinking that in the case of SV the beacon could only allow either:

'startMin', 'startMax', 'endMin', 'endMax' (for imprecise SV) 

or

'start', 'end'

but never all at the same time. 

Thanks,

Diana 

[Miro Cupak]

Hi Diana,

let me add the Beacon API mailing list, where they can help you.

Cheers,
Miro

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