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Association mapping with plink: what type of phenotypic data?

I want to know what kind of phenotypic data I can put in PLINK.

I have this phenotypic file (pheno1.txt):

enter image description here

I coded the sex like this: Sex (1=male; 2=female; other=unknown)

Everything is on a continuous scale. no missing values. The IID is the same as the one in the VCF file.

I ran this line: 

plink --file output_in_plink --pheno pheno1.txt --out run2

output_in_plink is the files that are named 

output_in_plink.ped
output_in_plink.log
output_in_plink.map

Coming from the command vcftools --vcf output.vcf --plink --out ./plink/output_in_plink

After, I ran this:

plink --file output_in_plink --pheno pheno1.txt --out run2

But it returns nothing except a log and a no sex file...

When I ran this:

plink --file output_in_plink --no-fid --pheno pheno1.txt --out run2

It tells me that there si an error:

ERROR: 
Problem with line 1 in [ output_in_plink.ped ]
Expecting 5 + 2 * 840907 = 1681819 columns, but found more

The end goal is to calculate an association mapping of the individuals coming from different populations (4 different species): 

plink --file output_in_plink --no-fid --no-parents --pheno pheno1.txt --all-pheno --assoc --maf 0.05 --out run1

But this is not working. Do you know how to solve this?

Maybe I should include the species?:

enter image description here

plink association mapping gwas snp vcf
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updated by Fabio Marroni Fabio Marroni • written by beausoleilmo beausoleilmo

1 answer

From PLINK user manual:

plink --file mydata --pheno pheno.raw --assoc --maf 0.05 --out run1
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written by Fabio Marroni Fabio Marroni

What's mydata? What's pheno.raw?

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written by beausoleilmo beausoleilmo

What's mydata? What's pheno.raw?

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written by beausoleilmo beausoleilmo

mydata=output_in_plink

pheno.raw=pheno1.txt

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written by Fabio Marroni Fabio Marroni

It seems to work but it returns nothing for F_A F_U and CHISQ (from the file run1.assoc). 

  1  CHR                    SNP         BP   A1      F_A      F_U   A2        CHISQ   
  2    0            C12915379:2          2    G       NA       NA    T           NA   
  3    0            C12330165:5          5    A       NA       NA    T           NA   
  4    0            C12485604:5          5    A       NA       NA    G           NA   
  5    0            C12707046:5          5    G       NA       NA    C           NA   
  6    0            C13160573:5          5    A       NA       NA    G           NA   
  7    0            C12336575:6          6    T       NA       NA    C           NA

It's saying here that I'm suppose to have a p-value: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml

The weird thing is that they are not proposing a phenotypic file here: 

plink --file mydata --assoc
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written by beausoleilmo beausoleilmo

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