Assigning locus to set of SNPs based on its chromosome position

Question

[iphoenix2100]

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

Answer 1

[Bert Overduin]

Hi,

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

Bert