Question: Location of intronic SNPs from exons
1
gravatar for BAGeno
8 months ago by
BAGeno120
BAGeno120 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 • 379 views
ADD COMMENTlink modified 8 months ago by Emily_Ensembl17k • written 8 months ago by BAGeno120
1

see Defining Precisely The Genomic Context Based On A Position

ADD REPLYlink written 8 months ago by Pierre Lindenbaum117k
3
gravatar for Jeffin Rockey
8 months ago by
Jeffin Rockey1.0k
Karimannoor
Jeffin Rockey1.0k wrote:

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

Please see option -d in particular

ADD COMMENTlink written 8 months ago by Jeffin Rockey1.0k
3
gravatar for cpad0112
8 months ago by
cpad011211k
India
cpad011211k 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 8 months ago • written 8 months ago by cpad011211k

@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 8 months ago by BAGeno120

HGVS documentation

ADD REPLYlink written 8 months ago by Emily_Ensembl17k
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