Question: Assigning locus to set of SNPs based on its chromosome position
0
gravatar for iphoenix2100
3.0 years ago by
iphoenix210030
European Union
iphoenix210030 wrote:

Hi all,

 

 

So I have this tab-delim file with information on (following columns)

SNP    CHR    POS   Allele1    Allele2    A.Freq1    Effect    StdErr    P.value

- Now I would like to assign the SNPs to its corresponding locus based on the chromosome position. 

As I am new in this field - i find it hard to even start in the right place. Will be great if someone can give some ideas/suggestions. Thanks in advance

IP

assembly genome • 990 views
ADD COMMENTlink modified 3.0 years ago by Bert Overduin3.6k • written 3.0 years ago by iphoenix210030
0
gravatar for Bert Overduin
3.0 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

Hi,

There are many tools that can do this, but my favourite is the Ensembl Variant Effect Predictor (VEP).

Bert

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Bert Overduin3.6k
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