How To Map Snp Profile From Dbsnp Build 131 To 132?

Question

[Edi]

Hi, I am having a SNP profile with novel SNP's from dbSNP 131 build, and I am planning to update it with new dbSNP 132 build. Can anybody guide me how to do this? Will it be easy to analyze chromosome wise? Thank you in advance.

[Pierre Lindenbaum]

what do you mean with "SNP profile" ?

Answer 1

[Jorge Amigo]

the most appropriate way of doing this would be by checking your SNP profile against the dbSNP merge file available on their FTP site, which would let you upgrade your rs codes as described here.

but are you only planning to upgrade variants present on dbSNP131, or do you also have novel variants that were not present on dbSNP 131 but you would like to see them on dbSNP132? in that case, and considering that dbSNP131 and dbSNP132 are both GRCh37/hg19 based, I think that the easiest way to do this would be to batch query directly any variation repository containing dbSNP132 data (dbSNP itself, Ensembl, ...) by the list of positions on your SNP profile, getting not only which of those dbSNP131 SNP positions are still present on build 132, but also which of those not annotated variants are now described on dbSNP132.

[Edi]

Thank you. I am also hoping to analyze the novel variants with dbSNP as well.

[Jorge Amigo]

there you go then. batch querying (either on the web or by using mysql scripts) would be the best option you may have.