Hello Mike, Your message got through; you do not need to be subscribed to the list to ask questions. And we generally reply-all, so you do not need to be subscribed to get an answer, either. For more information on the list: http://genome.ucsc.edu/contacts.html.
The genome sequence is identical for NCBI build 36.1 and 36.2, so the SNP positions should be the same for either build. See: http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html#36.2assembly LiftOver can be used to lift single base position ranges from hg18 to hg19 (GRCh37), but the results won't be perfect, as you might expect. It is also possible to get lists of SNP positions from dbSNP build 130 in hg18 and from dbSNP build 132 from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). However, to me it looks like the data you are looking at from the HapMap project has already been lifted to hg19/GRCh37. I see this in the README.txt file that is included in the tar file you link to: --- The map was generated by lifting the HapMap Phase II genetic map from build 35 to GRCh37. The original map was generated using LDhat as described in the 2007 HapMap paper (Nature, 18th Sept 2007). The conversion from b35 to GRCh37 was achieved using the UCSC liftOver tool. (etc.) --- Would you perhaps like to make a custom track of the HapMap SNP info instead? I see that the files look like this: Chromosome Position(bp) Rate(cM/Mb) Map(cM) chr1 55550 2.981822 0.000000 chr1 82571 2.082414 0.080572 chr1 88169 2.081358 0.092229 You could turn that into a BED format file (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) by changing those lines into: chr1 55549 55550 chr1 82570 82571 chr1 88168 88169 And then upload that as a custom track (hit the "add custom track" button under the main Genome Browser graphic). If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/19/11 2:50 AM, Mike Miller wrote: > I have map positions for Illumina SNPs that seem to be from NCBI Build > 36.2. I don't know how different those would be from 36.1, which seems to > be equivalent to hg18, but probably at least close enough for my current > purposes. I want to convert them to hg19 (GRCh37). The reason is that I > want to use the GRCh37 map here... > > http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz > > ...to get linkage map locations for the Illumina SNPs. > > I thought maybe the liftOver program can do this, but now I'm not so sure. > If I just had a file with a few million SNPs listed with their base-pair > positions in both hg18 and hg19, I could use that. > > Please cc me if you reply because I am not subscribed to this list. I > don't even know if my message will get through. The list was mentioned > here: > > http://genome.ucsc.edu/FAQ/FAQdownloads#download28 > > Mike > > -- > Michael B. Miller, Ph.D. > Minnesota Center for Twin and Family Research > Department of Psychology > University of Minnesota > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
