spliceai score

[jml96]

Hi,
I would like to understand why the scores obtain using spliceai script and in https://spliceailookup.broadinstitute.org/ are different from the ones provided in the file spliceai_scores.raw.snv.hg38.vcf.gz,downloaded from Illumina basespace,and required to run VEP spliceai plugin.
Thank you.

[bw2]

The difference is often because the precomputed scores were generated by running SpliceAI with a max distance of 50bp, while https://spliceailookup.broadinstitute.org/ has a default of 500bp.
. You can check if changing this to 50bp on the website resolves the difference.

Another less frequent reason is that the precomputed tables are based on Gencode v24, while https://spliceailookup.broadinstitute.org/ now uses Gencode v44. To check if Gencode transcript definitions changed for your gene of interest you could open older and newer Gencode versions in IGV using the File > Load from Server.. menu.

[jml96]

Thank you for your reply.
I will check this.

[jml96]

I have changed the maximum distance and now the spliceAI scores are consistent.
Thank you for the help.