hg38 splice ai file

[jsl-netizen]

Hi,
I'm currently trying to run Captain Achab and would like to know if you could please share or provide access to the custom hg38 annotation file for Annovar mentioned in the documentation.

It would really help ensure compatibility with the pipeline and reproduce your results accurately.

Thanks a lot for your time and for maintaining this great tool! 🙏

Best regards,

[thomasguignard]

Hello,

We use the custom annotation file within annovar command line through this argument : -xref my_custom_annotation_file.tsv
Sorry I can't provide it but I recommend to use the updater.sh script to create it: https://github.com/mobidic/AddDB_updater/blob/master/updater.sh

This custom file will be compliant with hg19 and hg38 since it is not related to genomic position, only gene name.

And I also recommend to perform the HGNC name check/update (quite long) on the gnomAD constraint file (commented here):
https://github.com/mobidic/AddDB_updater/blob/09825df35ca30ef364811f1ac914737e9a9ef16b/updater.sh#L42

[jsl-netizen]

Hi, sorry for the confusion in my previous message — I’d like to clarify my request.

In the README of the MoBiDiC Prioritization Algorithm (MPA), it is mentioned that:

“Update April 2019: spliceAI annotations now replace spidex. Waiting for spliceAI to be included in ANNOVAR, Files for this dataset in the proper format are available upon request (hg19 or hg38).”

I was referring specifically to these SpliceAI annotation files that were formatted for ANNOVAR (hg19 or hg38).
Could you please let me know how to obtain these files, or whom to contact to request them?

Thank you very much for your time and help!