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 Henn et al dataset, which you can download from their website.
There are 107 samples common from the HapMap (IDs start with NA) and 131 from HGDP (IDs start with HGDP).
Henn et al has two PED files. One for the Khoisan data and one for all Africa 55k SNP set. Unfortunately they have 31 San duplicated in both these PED files with same individual IDs but different family IDs (SAN and SAN_SA). So they do not get automatically merged per Plink procedures. Just remove all the ones with SAN_SA FID since they have fewer SNPs. All the IBD info etc is in this spreadsheet.
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