Ben Weisburd

The recommendation from SpliceAI authors is to ignore the masking property for junctions that are not the closest junctions to the variant. I'm not sure how to best address this...

Hi @Manuel-DominguezCBG If you uncheck the "masked scores" checkbox and rerun your search, you should see the results you expect. The help message for that checkbox explains the behavior you...

The way I understand it, for **donor gain** or **acceptor gain** predictions, when the predicted position (as shown in the "position" column) corresponds to the genomic location of a known...

Thanks for reporting this issue. SpliceAI-lookup uses Ensembl APIs to convert HGVS notation to `chrom-pos-ref-alt` before passing it to the SpliceAI model, so I've changed it to also show the...

Wow, this proved to be challenging and interesting to track down. My current understanding is that this isn't a bug, but is an inevitable consequence of assigning a single genomic...

I now think that, although insertions in repetitive regions make this problem more obvious (since it's common to see variants there with multiple equivalent representations), this isn't confined to repetitive...

A table of scores for inserted bases has now been added - for example @ https://spliceailookup.broadinstitute.org/#variant=13-21155151-C-CAGTTTTCTTTGTTGCTGACATCTCGGATGTTCTGTCCATGTTTAAGGAACCTTTTACTGGGTA&hg=38&bc=comprehensive&distance=500&mask=0&ra=1

There's now an automatic warning that appears for insertions that match both of these criteria: 1) the variant is an insertion of at least 2bp 2) its delta score is...

The table of scores has now been added. For example @ https://spliceailookup.broadinstitute.org/#variant=13-21155151-C-CAGTTTTCTTTGTTGCTGACATCTCGGATGTTCTGTCCATGTTTAAGGAACCTTTTACTGGGTA&hg=38&bc=comprehensive&distance=500&mask=0&ra=1

https://github.com/broadinstitute/SpliceAI-lookup/tree/master/annotations has scripts for this. See https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/update_SpliceAI_annotation_txt_files.sh