Why SpliceAI does not annotate variants in different transcripts as SpliceAI lookup does.

Question

[Manuel]

I can see how SpliceAI lookup provides splice annotation for the the main transcripts of the affected gene. For example for the variant

chr1 150531125 G A

There is annotation data for seven transcripts. However, reading the SpliceAI documentation I don't see an option that allows me to do this and therefore only the standard output is returned. For the previous example, the data is

SpliceAI=A|ADAMTSL4|0.09|0.00|0.05|0.61|-15|0|37|0

When using SpliceAI how can I know in what transcripts that annotation data refer to? or how can I get the full information.

It must be something obvious I am missing. I prefer to ask here first that in the github repo.

I am using SpliceAI 1.3.1 working in hg19.

Answer 1

[Manuel]

I have found the answer here

https://github.com/Illumina/SpliceAI/issues/112