SMARTPCA

Question

[Chanuka]

Hi,

I want to create a parameter file to use in SMARTPCA, i'm new to this how do i create the parameter file.

[Mwangana]

Hi Chanuka, did you manage to prepare the parameter file? Did you successfully run smartpca. I am able to prepare the parameter file but I can't run smartpca as the eigensoft package I have installed is not an ELF 64-bit LSB executable!

Answer 1

[pabe]

Take a look at this guide.

Your basic parameter file should look like this:

genotypename: <GENOTYPE_DATA>.geno

snpname: <GENOTYPE_DATA>.snp

indivname: <GENOTYPE_DATA>.ind

evecoutname: <OUT_FILE>.evec

evaloutname: <OUT_FILE>.eval

poplistname: <POPULATION_LIST_FILE>.txt

lsqproject: YES #this depends on if you have a lot of missing data

numoutevec: 4

numthreads: 1