About deletion and insertion queries

[christos...@saphetor.com]

Hello,

we are currently in the process of implementing our own Beacon and then participating in the beacon network.

I would like to ask about deletion and insertion allele parameters (D and I) that are being passed to the beacon network when a user requests for a deletion or insertion variant through the beacon network api.

How is this being transformed into a request back to a specific beacon? (is it the same value D or I passed?)

Another one... I also noticed that reference allele is not submitted as part of the request for a beacon network api query. Does the beacon network somehow query the specific beacon with the reference allele or is it up to the beacon to "know" the reference allele at the specific chromosome position if this parameter is not passed along the request... I know it is feasible to know the reference allele but I was just wondering whether this is part of the request parameters passed from the network to a specific beacon anyway.


Thank you

Christos Kopanos
Saphetot SA.

[Miro Cupak]

Hi Christos,

Beacon Network API is more similar to the older 0.2 version of the Beacon API (actually predates it). 0.2 beacons use D/I, so we simply pass it through (or convert to something like DEL/INS depending on the needs of a beacon).

The reference allele is not sent for a similar reason - 0.2 Beacon API does not support it. The latest Beacon API requires a reference allele, and we’re in the process of updating the Beacon Network to handle it. We should release this soon, so you can either wait, or implement the previous API version for now.

Hope this helps,
Miro

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