Question: Location of intronic SNPs from exons
1
gravatar for BAGeno
4 months ago by
BAGeno100
BAGeno100 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 • 257 views
ADD COMMENTlink modified 4 months ago by Emily_Ensembl16k • written 4 months ago by BAGeno100
1

see Defining Precisely The Genomic Context Based On A Position

ADD REPLYlink written 4 months ago by Pierre Lindenbaum115k
3
gravatar for Jeffin Rockey
4 months ago by
Jeffin Rockey980
Karimannoor
Jeffin Rockey980 wrote:

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

Please see option -d in particular

ADD COMMENTlink written 4 months ago by Jeffin Rockey980
3
gravatar for cpad0112
4 months ago by
cpad011210k
India
cpad011210k 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 months ago • written 4 months ago by cpad011210k

@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 months ago by BAGeno100

HGVS documentation

ADD REPLYlink written 4 months ago by Emily_Ensembl16k
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