I got the 1000genomes data a couple of weeks ago. Trying to convert it from VCF to PED format using vcftools was a complete disaster. Then Dienekes sent me a conversion script which was more than a hundred times faster.
1000genomes will have 100 Assamese Ahom, 100 Kayadtha from Calcutta, 100 Reddys from Hyderabad, 100 Maratha from Bombay and 100 Lahori Punjabis later this year. Right now, the new populations (other than HapMap) are British, Finns, Han Chinese South, Puerto Ricans, Colombians, and Spaniards.
I removed all the 660 samples which were common with the HapMap data. Also, there were 31 pairs with high IBD values. The list of IBD/IBS values and the samples I removed can be seen in the spreadsheet.
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