Question: Location of intronic SNPs from exons
1
gravatar for BAGeno
3 months ago by
BAGeno80
BAGeno80 wrote:

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?

position introns exon vep • 201 views
ADD COMMENTlink modified 3 months ago by Emily_Ensembl16k • written 3 months ago by BAGeno80
1

see Defining Precisely The Genomic Context Based On A Position

ADD REPLYlink written 3 months ago by Pierre Lindenbaum113k
3
gravatar for Jeffin Rockey
3 months ago by
Jeffin Rockey720
Karimannoor
Jeffin Rockey720 wrote:

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

Please see option -d in particular

ADD COMMENTlink written 3 months ago by Jeffin Rockey720
3
gravatar for cpad0112
3 months ago by
cpad01129.3k
India
cpad01129.3k wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by cpad01129.3k

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

ADD REPLYlink written 3 months ago by BAGeno80

HGVS documentation

ADD REPLYlink written 3 months ago by Emily_Ensembl16k
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