Hello, The SNP build is the official one. If a SNP is missing, I would definately look into why by examining the records at NCBI. There could be many reasons it is missing ... but the one you want to watch out for is that it is not longer considered a SNP.
http://www.ncbi.nlm.nih.gov/SNP/ Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Pattle Pun" <[email protected]> wrote: > From: "Pattle Pun" <[email protected]> > To: [email protected] > Sent: Thursday, October 22, 2009 2:23:57 PM GMT -08:00 US/Canada Pacific > Subject: hg18/hg19 differences > > ** High Priority ** > ** Reply Requested When Convenient ** > > Dear Jennifer, > > Thank you in advance for your prompt responses as you did in the > past. > > I was using your hg18 version (march 2006) of HGP to search for all of > my SNP's (see below) > > rs12446940 > rs2238419 > rs2283484 > rs2283487 > rs2283489 > rs4786446 > > above SNP's not selected by the Haplotter program : > http://hg-wen.uchicago.edu/selection/haplotter.htm > > rs11648728 > rs8060585 > rs4984682 > rs3765316 > rs7404985 > rs7404049 > rs7184950 > > above SNP's selected by the Haplotter program : > http://hg-wen.uchicago.edu/selection/haplotter.htm > > However, none of these SNP's can be identified in the hg19 version > (Feb. 2009) on your browser: > http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19&hgsid=145863072 > > They are still available on the hg18 versionon your browser: > http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=145863072&clade=mammal&org=Human&db=hg18 > > Are there some systematic changes you made in hg19that are totally > different from hg18 to make this happen?Should we stick with hg18 once > we started using them instead of switching to hg19? > > I believe Haplotter is still using the Mar. 2006 version of HGP for > their operation. > > Please let me know at your earliest convenience, before Tues. 10/27 if > possible since I am running another set of data through your browser. > > Pattle.P.T.Pun, Ph.D. > Professor of Biology, > Wheaton College, > Wheaton, IL 60187 > phone: 630-752-5303 > fax: 630-752-5996 > email: [email protected] > http://www.wheaton.edu/Biology/faculty/ppp/index.html _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
