Hello Adrian, We do host data for those two cell lines in our "Genome Variants" track (in the "Variation and Repeats" track group). The tables are available for download in our pgSNP format: http://genome.ucsc.edu/FAQ/FAQformat.html#format10
They are on our downloads server here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA12878.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA19240.txt.gz However, those variant calls were taken from 1000Genomes' Dec. 2008 release, so you might prefer to get newer data. One of our engineers suggests getting more recent VCF files directly from 1000Genomes: http://www.1000genomes.org/ . The front page always lists the latest data release -- search there for recent VCF. Then click through to the project's browser (http://browser.1000genomes.org/index.html), and click the "Individual genotypes" link. On the left side of the new page, there is a "Get VCF data" button that pops up a form where you can specify a VCF file and ID's of individuals (in this case NA12878 and NA19240) to extract from the file. Unfortunately the form's default VCF file does not include NA12878 nor NA19240... also, note that 1000 Genomes VCF files are often for only one chromosome (chr6 for the form's default VCF file). So choose VCF file with care before using that form. These pilot project release files have data for NA12878 and NA19240: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/CEU.trio.2010_03.genotypes.vcf.gz ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/YRI.trio.2010_03.genotypes.vcf.gz It is possible to use these URLs to make custom tracks in the Genome Browser. Full instructions for making a VCF custom track from scratch are here: http://genome.ucsc.edu/goldenPath/help/vcf.html but you would only need to paste some track definitions such as these into the custom tracks page (http://genome.ucsc.edu/cgi-bin/hgCustom) to use these files: track type=vcfTabix name="CEU" bigDataUrl=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/CEU.trio.2010_03.genotypes.vcf.gz track type=vcfTabix name="YRI" bigDataUrl=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/YRI.trio.2010_03.genotypes.vcf.gz Make sure all of the information for each track is on a single line. The tracks won't necessarily load if there are problems on NCBI's ftp server. (When I tried it just now, one loaded and one did not.) If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 1/27/12 1:59 PM, Adrian Johnson wrote: > Hi: > Is it possible to download from genomebrowser all the variant calls > either a VCF or BED file for HapMap cell lines > GM19240 and GM12878? > > thanks > -Adrian > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
