Hello, We are not exactly clear about the dataset you are referring to. Are you looking for a particular published dataset (we are not familiar with one with the name "Rare SNPs")? Or are you looking for a track with defined allele frequencies - already filtered below a certain threshold?
We do have some tracks for datasets with sufficient sample sizes to estimate frequency within some populations: HGDP Alleles contains frequencies in 53 populations worldwide, and HapMap SNPs includes allele counts (even better -- you know the sample size in addition to freq) for 11 populations. The aim of the 1000 Genomes project is to catalog all variants with a minor allele frequency of at least 1% in the genome, and at least 0.5% within genes (http://1000genomes.org/bcms/1000_genomes/Documents/1000Genomes-NewsRelease.pdf). The pilot project is in the analysis phase, and the results should be published next year. If there is a particular published dataset that you want to view in the browser, that is not currently contained, the option to create a custom track available. Read the methods for the dbSNP track, obtain the correct data and perform an alignment, or obtain the genomic locations directly, if available. Then load the data in one of our data formats. If you need pointers to BLAT or Custom track help that you cannot locate in the FAQ, or just have questions as you work through the process, please let us know, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Gundala Viswanath" <[email protected]> wrote: > From: "Gundala Viswanath" <[email protected]> > To: [email protected] > Sent: Wednesday, December 2, 2009 6:42:46 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Rare SNPs Annotation in UCSC? > > Hi, > > I have no problem downloading human (hg19) snp annotation here: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp130.txt.gz > > Currently I am looking for the same annotation file for Rare SNPs. > Is there a way to download them that in UCSC? > > > - G.V. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
