Question: Eigensoft Error - bad geno
0
gravatar for nrcolumbia
3.8 years ago by
nrcolumbia0
nrcolumbia0 wrote:

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 • 1.8k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 3.8 years ago by nrcolumbia0

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?

ADD REPLYlink written 3.8 years ago by WouterDeCoster44k

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!

ADD REPLYlink written 3.8 years ago by nrcolumbia0

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

ADD REPLYlink written 3.8 years ago by WouterDeCoster44k

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

ADD REPLYlink written 3.8 years ago by nrcolumbia0
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