false wt calls in N regions

[ulfschaefer]

HI there

We are noticing an issue where Ns in the N gene are called as wild type.

The attached zip contains an example of an alignment and the calling.json. It produces no-detect for D63G and R203M in the N gene at ref positions 28461 and 28881 respectively. These are clearly called as N in the sequence.

As a consequence of this, this sample does not get called as a Delta variant, because the definition allows no wildtypes. We have multiple example of this happening.

(My guess is that this is because the N region here extends without interruption all the way to the 3' end of the genome. Maybe.)

issue.zip

Thanks for your help
Ulf - UKHSA