Question: Changing Build From 37 To 36 In Snp Data
gravatar for GabrielMontenegro
6.1 years ago by
United Kingdom
GabrielMontenegro540 wrote:

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

genome plink snp • 4.3k views
ADD COMMENTlink modified 6.1 years ago by Ryan D3.3k • written 6.1 years ago by GabrielMontenegro540

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

ADD REPLYlink written 6.1 years ago by zx87549.1k

you can try ucsc genome browser:variation and repeats track

ADD REPLYlink written 6.1 years ago by ancient_learner620
gravatar for Ryan D
6.1 years ago by
Ryan D3.3k
Ryan D3.3k wrote:

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.

ADD COMMENTlink written 6.1 years ago by Ryan D3.3k
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