Check whether two GWAS are from the same ancestry

Question

[kl]

Hi all,

I've performed a meta-analysis and want a way of seeing whether the people in my GWAS all have European ancestry by checking the allele frequency compared to 1000G. Is there any program that can check for differences for large datasets?

Thanks

Answer 1

[Kevin Blighe]

Check how they line up on a PCA bi-plot via this tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

You will have to merge your dataset with the 1000 Genome Dataset prior to performing the PCA command.

Kevin