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Location of intronic SNPs from exons

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?

exon position introns vep
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updated by Emily Emily • written by BAGeno BAGeno

2 answers

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

Please see option -d in particular

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written by Jeffin Rockey Jeffin Rockey

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.

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written by cpad0112 cpad0112

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

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written by BAGeno BAGeno

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