Question

SMARTPCA

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2.5 years ago

Chanuka • 0

Hi,

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

SMARTPCA • 1.2k views

ADD COMMENT • link updated 2.2 years ago by pabe ▴ 30 • written 2.5 years ago by Chanuka • 0

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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!

ADD REPLY • link 2.2 years ago by Mwangana • 0

score 0 · Answer 1 · 2022-08-29

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