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How do I compute principal components using only a subset of SNPs but then run EIGENSTRAT using the full set of SNPs?

April 26, 2017components compute eigenstrat Principal run SNPs subset

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How do I compute principal components using only a subset of SNPs but then run EIGENSTRAT using the full set of SNPs?

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If using smartpca.perl, then run smartpca.perl on reduced data set and then run EIGENSTRAT on full data set. If using smartpca, then run smartpca on reduced data set, then run evec2pca.perl to produce .pca file, then run EIGENSTRAT on full data set. Details in POPGEN/README and EIGENSTRAT/README.