I have list of intronic SNPs. I used VEPP to find in which intron a specific SNP is located. But I want to find how many base pairs is that intronic SNP away from exon. Is there a tool to do this?
see Defining Precisely The Genomic Context Based On A Position
You should be able to do that using bedtools closest (link)
Please see option -d in particular
when you use VEP to annotate and use HGVS, csyntax should give you the distance either upstream or downstream of coding position, for each transcript.
@cpad0112 I tried your suggestion. And got something like this. HGVSc=ENST00000234961.6:c.228-10520A>C Could you please explain this?