Which database can be used to identify canonical splice site altering for ANNOVAR?

Question

[Shicheng Guo]

Hi All,

Which database can be used for ANNOVAR to identify canonical splice site altering? I find ANNOVAR can identify stop-gain and stop-lost very easily. However, I didn't find any database for ANNOVAR to identify canonical splice site altering.

Thanks.

table_annovar.pl ./annovar/gnomad.exomes.r2.1.sites.chr22.rec.vcf.avinput ~/annovar/humandb/ --thread 4 -buildver hg19 --csvout -out ./annovar/chr22 -remove -protocol refGene,dbnsfp33a,gwasCatalog,wgRna,targetScanS,tfbsConsSites -operation gx,f,r,r,r,r -nastring . -otherinfo -polish -xref ~/humandb/gene_fullxref.txt

[lincaijin1994]

Hi, I have the same question. Have you found the solution? In some papers, they defined the canonical splice variants as those +/- 1 or 2. Also, some literatures stated that splice_site variants in the penultimate or the last exons were excluded. I dont know how to identify splice_site variants in the penultimate or the last exons.