SpliceAI Plugin: Masked Scores available?

[stefandiederich]

Hi,
my colleague asked me if it is possible to annotate the masked SpliceAI values instead of the raw ones like you can do at spliceAI lookup homepage.
In the plugin description I could not find any option to enable this. Is it somehow possible to get these masked scores for annotation?

Bests
Stefan

[dglemos]

Hi @stefandiederich,
to annotate the masked scores you only have to input the masked file into the plugin.
Example:
--plugin SpliceAI,snv=/path/to/scores.masked.snv.hg38.vcf.gz,indel=/path/to/scores.masked.indel.hg38.vcf.gz

You can use the files provided by Illumina or you can use the scores calculated for MANE transcript in the following link (only available for snv):
http://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_plugins/