Issue with spliceAI output for some indels

[HLSZim]

Hi,

I've run into difficulty getting spliceAI output for a couple of indels. The API appears to be pulling the correct genomic position and variant nomenclature for my input variant, but I see periods in the output instead of spliceAI scores and positions. I've attached an image for NM_005591.3(MRE11A):c.1225_1225+1delinsCA to illustrate this issue. If I change this to NM_005591.3(MRE11A):c.1225_1225+1del or NM_005591.3(MRE11A):c.1225delinsC, I do get scores. A similar issue is seen with
NM_000051.3(ATM): c.6808_6810delinsTTT and NM_000038.5 (APC):c.5267_5268delinsTG.

Is this user error on my end?

Thanks,
Heather

[bw2]

Hi Heather, thanks for posting this issue.
I've added an error message for this, since SpliceAI doesn't currently process these kinds of variants.

[bw2]

MNP support has now been implemented (via https://github.com/bw2/SpliceAI) thanks to @kdahlo