Hi Todd, The hg18ToHg19 file is lifting to the GRCh37, not to one of the patches.
It is lifting to the same assembly that we show in the Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19). More details for the assembly can be found at the link to NCBI on that page: http://www.ncbi.nlm.nih.gov/genome/assembly/2758/. It looks like GRCh37.1 (or GRCh37.p1) is the name of the first patch. The hg18ToHg19 file is going to GRCh37 (without a revision/patch number). Incidentally, the downloads link you are using is for our test server, "hgdownload-test." In this case, the file on the test server is identical to the one on our regular server: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ but, in general, the test server contains data that has not been reviewed and that may never be released. You may want to switch to the regular server. If you were intending to use the test server, you should be aware of the caveats. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/13/12 10:12 AM, Todd Green wrote: > Hello, > > Which assembly is the hg18tohg19 liftover file lifting to? Is it GRCh37.1 > or one of the patches? I notice that the date of the file is July 26 2010 > not Feb. 2009. > > > http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/liftOver/ > > hg18ToHg19.over.chain.gz<http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz> > 26-Jul-2010 11:25 > 137K > > > Thanks for your time, > Todd > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
