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Wing Genealogist
08-26-2017, 06:42 PM
I am exploring online NGS/WGS datasets too look at the frequency of R-U106 and its subclades. To date, I am aware of the Open Search project at: https://search.hli.io/?q= and the Swedish Genome project at: https://swegen-exac.nbis.se/

Is anybody aware of other online NGS/WGS datasets which would include either number of individuals or percentage of male individuals within the dataset who are positive for Y-SNPs?

Both of these datasets require users to ask for (and receive) permission to access the dataset. Neither dataset utilizes the SNP names (such as U106) but use the ChrY: position to identify them.

The SweGen Project uses the Hg19 (Build 37) positions which can easily be found at YBrowse http://ybrowse.org/gb2/gbrowse/chrY/?
But the Open Search dataset uses the newer Hg38 (Build 38) positions.

Does anyone know of an easy way to find the Hg38 position from Hg19 position data? I am aware of the hg Lift Over utility at: https://genome.ucsc.edu/cgi-bin/hgLiftOver but I have difficulty using this utility. [EDIT: I have received help with obtaining Hg38 data already]

BTW: The U106 Tree can be downloaded from: https://app.box.com/s/afqsrrnvv2d51msqcz2o