Can anyone recommend a good software for doing Principal Component Analysis from data in VCF file format, or the most straightforward format to convert the VCF into for doing PCA. I hear that Plink is quite suitable for this. I also have some experience using eigenstrat for SNP data but have no experience using eigenstrat with whole genome VCF encoded data. Any tips or experience appreciated.
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. According to the documentation, it runs 10-45x faster than EIGENSTRAT (v3.0) and PLINK (v1.07) respectively.
Update (Oct 2014): The package seems to be moved to GitHub (link)