I'm having some trouble creating PCA plots from my combined VCF file, or even the HapMap sample files for that matter.
PLINK tools have gotten me to a format suitable for EIGENSTRAT, but I am not able to use the smartpca package correctly. There is a script called smartpca.pl that calls a nonexistent binary smartpca from the package, and I have not been able to locate this binary. I haven't been able to make the binary compile either, and all in all I'm feeling pretty frustrated with the whole thing :( What I am really looking for is anyone's much more simple script/solution for PCA plot creation from VCF format, or some more helpful documentation than what is found on the tool's website.
EDIT: After re-downloading EIGENSTRAT again, I now have a smartpca file! And now I have a plot! Question for scripts still stands though..