I get requests from time to time about sharing my Reference 3 dataset. I use a few datasets which I am not allowed to redistribute, but most of the others are actually public and the main issue is to convert them to plink format and merge them.
I have released code for the conversion already but to make the task even easier I am letting you guys know that I already released a subset of my dataset a long time ago. Razib wrote about it and added the detailed instructions on using that dataset.
So here's the link to the dataset which contains about 30,000 SNPs and almost 4,000 individuals from HapMap, HGDP, SGVP, Behar et al and Xing et al.
I haven't done any admixture dendrograms in a while, so I thought you guys might be interested.
This uses admixture results using Reference 3. As usual, I used complete linkage for the hierarchical clustering.
Let's look at the dendrogram using regular Euclidean distance measure between admixture results.
I also decided to use chi squared distance measure to do the clustering.
PS. Any thoughts on the trees based on two different distance measures?
Here are the admixture results using Reference 3 for Harappa participants HRP0151 to HRP0160.
You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.
Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.
If the above interactive charts are not working, here's a static bar graph.
There are several interesting participants here. HRP0151 is a quarter Nepalese and his/her results are actually quite odd. The East Asian ancestry shows up as Native American which is possible. I wonder if the quarter Chinese ancestry is not Han but rather some other Chinese ethnicity.
HRP0155 is Sri Lankan Sinhalese and has a lower Onge component than I expected.
HRP0158 is my Dad and has similar results as me (HRP0001).
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