donwload dbSNP131 in BED-format

[Lien]

Hi all,

I am studying SNVs from Illumina paired-end data. I was wondering if I could make an overlap between my identified SNVs and the SNPs that are already known. In order to do that, I would need a BED-formate with the (at least) 4 columns:
Chr
Position (zero-based)
Position (one-based)
SNIP ID (rs-name).

I already looked at the UCSC and the NCBI website and I find there the SNPs in different files, per chromosome, but with a lot of additional information. Is there some shortcut to obtain the data I want, or do I need to download each file separately, then merge them, and then delete all the information I'm not interested in ?

Thanks a lot!
Lien

[epigen]

There is the whole dbSNP (snp131.txt.gz) at UCSC downloads:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

but to make a BED file you have to reorder/extract the columns (easy way e.g. with awk).

Barbara

[Lien]

Thanks a lot!