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Eigensoft Error - bad geno

Hi,

I am attempting to create PC's using Eigensoft but keep getting this error: 

fatalx:
(getpedgenos) "filename".ped bad geno I
Aborted

Could anyone help me understand what could be going wrong here? I am using pruned .map files. Here is the script:

genotypename:    trial.ped
snpname:         trial.map
indivname:       trial.ped
outputformat:    EIGENSTRAT
genotypeoutname: trial.eigenstratgeno
snpoutname:      trial.snp
indivoutname:    trial.ind

Thank you!

pca eigensoft
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updated by Biostar Biostar • written by nrcolumbia • nrcolumbia

Kinda hard to make a guess without seeing your data, but based on the error message I suspect that one of your genotypes is encoded as "I" in your .ped file. Does that make sense?

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written by WouterDeCoster WouterDeCoster

Thanks for the reply. Do you mean that for a particular sample, instead of alleles there may just be an "I" represented in the .ped file? Do you know how I may go about testing for this? Thanks again!

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written by nrcolumbia • nrcolumbia

I would suggest a simple grep grep -w "I" but I don't know your operating system.

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written by WouterDeCoster WouterDeCoster

Yes - I found the "I"s. Thanks for your help!

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written by nrcolumbia • nrcolumbia

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