Location of intronic SNPs from exons

Question

[BAGeno]

Hi,

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?

[Pierre Lindenbaum]

see Defining Precisely The Genomic Context Based On A Position

Answer 1

[Jeffin Rockey]

You should be able to do that using bedtools closest (link)

Please see option -d in particular

Answer 2

[cpad0112]

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.

[BAGeno]

@cpad0112 I tried your suggestion. And got something like this. HGVSc=ENST00000234961.6:c.228-10520A>C Could you please explain this?

[Emily]

HGVS documentation