I would like to know if there is any way to find more detailed information about the mutations that are annotated as splice site: does it affects donor or acceptor site, etc.
Do you consider only mutations in the consensus sequence or also mutations elsewhere that have been shown to affect the splicing process?
I wonder if the detailed information about the mutations eg. in the VCF format is accessible (Looking for VCF files of CCLE mutation data).
Unfortunately we do not generate any further information on the splice sites beside what you can find in the maf file. The splice site mutations are mutations that occur in the splice sites, and do not include mutations elsewhere that may affect splicing.
Thank you for your answer!
Are the splice site mutations annotated based on the RNA-seq data generated by DepMap/CCLE or are they simply tagged based on GENCODE or GTEx annotations?
No, these annotations are not based on RNAseq data. We rely on WES/WGS mutations and Oncotator annotations using the following database version:
gs://firecloud-tcga-open-access/tutorial/reference/oncotator_v1_ds_Jan262014.tar.gz
