unannotated SNP ids

Question

[m_02]

Hi all,

I have a list of unannotated SNPs, I want to find those genes which are present 10kb upstream and downstream of that unannotated SNP.

Thanks in advance

[Pierre Lindenbaum]

see How To Map A Snp To A Gene Around +/- 60Kb ?

Answer 1

[iraun]

If I've understood correctly your question, I'd suggest you the following workflow:

1. Take the positions of those unannotated SNP.

2. Create a bed file with:

   SNP_chromosome    SNP_position-10000    SNP_position+10000
   

3. Create gene .bed|.gtf|.gff3 file with gene coordinates.
4. Intersect (bedtools intersect) these two files.

Answer 2

[Emily]

You can use the Ensembl VEP for this. To get variants 10kb up and downstream you'll need to alter the upstream/downstream distance to 10kb, which you'll find in the options.