Changing Build From 37 To 36 In Snp Data

Question

[GabrielMontenegro]

I am working with genome wide SNP data and to use a specific program I need to change the positions of my SNPs from Build 37 to 36.

Is there somewhere a list of all the rs numbers with their according positions in Build 36?

I tried downloading the HAPMAP3 data (I used the MAP file, plink format) but not all my SNPs were present there, so when I used a script to change them I got a lot of gaps.

Thanks in advance

[zx8754]

This post might be relevant: Converting genome coordinates from one genome version to another (UCSC liftOver, NCBI Remap, Ensembl API)

[ancient_learner]

you can try ucsc genome browser:variation and repeats track

Answer 1

[Ryan D]

You can get a list of all rs numbers with their positions in hg18/build 36 [here] at the UCSC Genome Browser's Table Browser[1]. These contain the dbSNP entries from snp130, which I understand is the last build mapped to hg18/b36. The newer entries are mapped to hg19/b37. Just adjust the entries in the table browser to update to the latest dbSNP builds.