Question: Location of intronic SNPs from exons
1
gravatar for BAGeno
4 weeks 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 • 148 views
ADD COMMENTlink modified 4 weeks ago by Emily_Ensembl15k • written 4 weeks ago by BAGeno80
1

see Defining Precisely The Genomic Context Based On A Position

ADD REPLYlink written 4 weeks ago by Pierre Lindenbaum111k
3
gravatar for Jeffin Rockey
4 weeks ago by
Jeffin Rockey660
Karimannoor
Jeffin Rockey660 wrote:

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

Please see option -d in particular

ADD COMMENTlink written 4 weeks ago by Jeffin Rockey660
3
gravatar for cpad0112
4 weeks ago by
cpad01128.3k
India
cpad01128.3k 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 4 weeks ago • written 4 weeks ago by cpad01128.3k

@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 4 weeks ago by BAGeno80

HGVS documentation

ADD REPLYlink written 4 weeks ago by Emily_Ensembl15k
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