liftOver UCSC and rs number conversion

Question

[dora]

UCSC liftOver can lift genome positions (also chromosomal position) from hg18 to hg19, but it doesn't convert the rs numbers. For rs numbers from old to new builds can also be changed. Is there any way to solve this?

Answer 1

[Pierre Lindenbaum]

http://genome.sph.umich.edu/wiki/LiftOver

Lift dbSNP rs numbers

rs number is release by dbSNP. UCSC also make their own copy from each dbSNP version. Be aware that the same version of dbSNP from these two centers are not the same. When we convert rs number from lower version to higher version, there are practically two ways. Use RsMergeArch and SNPHistory

It is necessary to quickly summarize how dbSNP merge/re-activate rs number:

1. when different rs number are found to refer to the same SNP, then higher rs number will be merged to lower rs number, and the merging will be recorded in RsMergeArch.bcp.gz.
2. when rs number have to be retracted, rs number will be recorded in SNPHistory.bcp.gz
3. a retracted SNP can be re-activated in SNPHistory.bcp.gz by adding comment

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[dora]

@Pierre, thanks. I did use liftRsNumber.py from http://genome.sph.umich.edu/wiki/LiftOver to lift a list of rs numbers (hg18 to hg19, about 400k SNPs from 2010 or earlier), do you think it is normal that all SNPs are unchanged? Along with the latest version of RsMergeArch and SNPHistory. To compare with the results by using UCSC liftOver, I lifted the same list of SNPs and found that there are a few thousands of SNPs unlifted.