Tools/Script For Taking A Combined Vcf All The Way To A Pca Plot?
0
0
Entering edit mode
11.1 years ago
onter ▴ 170

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..

pca vcf analysis • 3.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 3151 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6