Hello, Ms. Al-Hasani, The human NCBI36 (hg18) assembly has SNPs through dbSNP version 130. For any SNPs added after that, (dbSNP ver 135), you could, indeed, use liftOver, as you suggest, to get the coordinates from hg19 back to hg18. Most SNPs from hg17 are likely to be already in the hg18.snp130 table. It is recommended that you try to use the hg19.snp135 table if you can, however.
You can download the hg18.snp130 from this location: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz and for hg19 from the analogous location. If you extract a list of rs numbers that exist in snp135 but not 130, you can feed that to liftOver (it will be large). regards, --b0b kuhn ucsc genome bioinformatics group On 1/17/2012 1:41 AM, Hoor Al-Hasani wrote: > Dear ladies and gentlemen, > I'm working on SNPs from different versions (35,36,37) and would like to > work with their IDs and positions based on 36 only. As I'm new to this, > I'm not sure if liftOver can do or how! > Could you please help? > > Thank you very much in advance > Ms. Al-Hasani > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
