Hope you can help on the population content in the HGDP panel
Yu Liang
Dear Madam/Sir,
I have been struggling to utilize the data from your HGDP allele frequency database for a while. I am dying to use the population frequencies data listed in your table scheme (http://genome.ucsc.edu/cgi-bin/hgTables). I searched the web and found that people had asked this same question 6 years ago and to my surprise the feedback your staff provided at that time was extremely vague without a straightforward answer, and 6 years later this page is still lack of this information. There are numerous links I can find either from your website or from that feedback, or from other places that I can google, but neither of them would provide a definitive answer to how the population frequencies data will match with. You can understand that any mismatch between these frequencies with the actual populations will cause unimaginable consequences to any analysis, so why isn’t the exact populations that match the frequencies in this database/table provided in the exactly same place at this page? Could you do that, or provide me that matching list of populations? Thanks so much.
Best regards,
Yu Liang
Yu Liang, Ph.D.
Director, Clinical Biomarkers
Calithera Biosciences
343 Oyster Point Blvd, Suite #200
South San Francisco, CA 94080
Tel: 650-870-1091
Fax: 650-588-5272
E-mail: yli...@calithera.com
Christopher Lee
Hi Yu,
Thank you for your question about HGDP population information. The population frequencies listed in the hgdpGeo table are listed in order of how they are displayed on an item's details page from the browser.
You can click on any of the items in the following session to bring up it's details page, and obtain a list of population data:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg18HGDPFreqClick
For example, here is the details page for one of the items in the
track, rs6653441, where you can see populations listed next to the
allele frequencies:
http://genome.ucsc.edu/cgi-bin/hgc?c=chrX&l=151073053&r=151383976&o=151103822&t=151103823&g=hgdpGeo&i=rs6653441&db=hg18
Please note that the example I have provided is for the Human hg18 assembly. If you are interested in an assembly other than hg18 you will have to visit the details page for an item in the hg19 hgdpGeo track to make sure the populations used are the same.
You might also be interested in the underlying data files we used to generate the track (the chr*.strat.gz files):
http://hgdp.uchicago.edu/data/Alfreqs/
These files explicitly list the population in each data line like so:
1 rs3094315 Brahui C T 0.26 13 50
I hope this was helpful, please let us know if you have any further questions!
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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Yu Liang
Hi Christopher,
This is really helpful. Thank you so much.
Best regards,
Yu