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Question: EIGENSOFT: CONVERTF ignoring samples
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Hi, the CONVERTF program in EIGENSOFT package is ignoring few samples and not calculating their principal components.

I am seeing this in my terminal when executing CONVERTF.

genetic distance set from physical distance

Sample1 ignored
Sample2 ignored
Sample3 ignored


Samplen ignored

genotype file processed
numvalidind: 21 maxmiss: 21001
packedancestrymap output

end of convertf run

Usually, it says ignoring all samples and then outputs the principal components for all the samples. I am just inputting the .PED and .MAP files in par.PED.EIGENSTRAT. It'd be great if anybody can give me some insight on this.



ADD COMMENTlink 4.3 years ago aritra90 • 40 • updated 4.3 years ago Philipp Bayer 6.1k
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I've ran into this one before - the EIGENSOFT FAQ has it, too:

Question: convertf decides to "ignore" all my samples. Why?
Answer: A likely reason is that you are using a "fam" or "ped" file with a funny value (0, 9 or -9) in column 6. Try setting column 6 to 1.

(Column 6 is the phenotype as far as I remember, and it has no effect on the PCA results)

ADD COMMENTlink 4.3 years ago Philipp Bayer 6.1k
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Yes, I saw the same just right after posting :P

Thanks, Philipp, it works now!

ADD REPLYlink 4.3 years ago
• 40
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Although the answer says that "Try setting column 6 to 1." I assume that it does not influence PCA results at all?

ADD REPLYlink 14 months ago
Phoenix Mu
• 0
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If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA

ADD REPLYlink 14 months ago
Philipp Bayer

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