Behar Redo

As part of my effort to create one big reference dataset for my use, I have been going over all the datasets I have and make sure there's no duplicates or relatives or any other strange things that could cause issues with my analysis.

So I went back to the Behar et al dataset, which you can download from the GEO Accession website.

I found three set of duplicates and two pairs with very high identity-by-descent values, which I calculated using Plink. You can see the samples with PI_HAT greater than 0.5 in this spreadsheet. PI_HAT is the proportion IBD estimated by plink. Notice also that all these pairs also have high IBS similarity (the DSC column), more than 83% similar.

The five samples I have removed as a result of this are listed in this spreadsheet.


  1. Relatives in Datasets | Harappa Ancestry Project - pingback on February 6, 2012 at 6:11 pm

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