Running Smartpca

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10.0 years ago

jmbarton37 • 0

I'm new to using eigenstrat and smartpca could someone give me an example of an appropriate parameter file? The one I designed only partially works and I'm not sure what else it needs.

---------Script text-----------

Genotypename: geno.EIGENSTRAT

snpname: QC1.snp

indname: QC1.ind

evecountname: QC1ev

evaloutname: QC1evo

outputformat: EIGENSTRAT

genotypeoutname: geno_out

snpoutname: QC1_out

indivoutname: QC1_out

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ADD COMMENT • link updated 10.0 years ago by kipp ▴ 50 • written 10.0 years ago by jmbarton37 • 0

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Can you be more clear what is going wrong? Your param file seems fine, though I think it should be "indivname"

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by kipp ▴ 50

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when entered I get

fatalx:
(getindivs) NULL indivfname

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by jmbarton37 • 0