Hi Randeep, These files are from the "Genome Variants" track on hg18 and hg19. If you go to the main Genome Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks) for either assembly, scroll down to the "Variation and Repeats" section, and click on the blue track name (the "Genome Variants") link, you will see a complete description of the track, including links to the publications for each dataset (where you can find the methods used).
The tables in the track were originally mapped to the hg18 assembly and were lifted to hg19 coordinates. See this note of caution about lifted data: http://genome.ucsc.edu/goldenPath/help/hg18ToHg19LiftOver.html The files you link are actually not exactly the same. I would expect them to have many identical entries, though. -- Brooke Rhead UCSC Genome Bioinformatics Group On 05/22/11 21:42, Randeep Singh wrote: > Hi, > > These are the personal genome variants links on UCSC. > Does anyone has the knowledge from which aligner/variant caller these were > called? > > > > *hg19:* > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA12878.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA12891.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA12892.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgNA19240.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgSjk.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgVenter.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgWatson.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgYh1.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgYoruban3.txt.gz > > > > *hg18:* > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgNA12878.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgNA12891.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgNA12892.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgNA19240.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgSjk.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgVenter.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgWatson.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgYh1.txt.gz > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/pgYoruban3.txt.gz > > > > > > Also, NA12891, NA12892, NA19240, Sjk, Watson and Venter have same files for > hg19 and hg18 > > > > Thanks and regards, > > Randeep > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
