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How should the data be formatted to run an association mapping in PLINK?

I'm trying to run a plink command to make an association mapping.

I created plink related files like this for the genetic files: 

vcftools --vcf output.vcf --plink --out ./plink/output_in_plink

And I was trying to create phenotypic files in PLINK with this: 

plink --file output_in_plink --pheno pheno.txt

But it returns nothing exceptional.

My phenotype file looks like this: 

FID            IID        sex   tars wingc mass mbl mbw mbd
fortis         JP3162_for 2     21.3 74.2 15.8 10.34 8.76 9.51
fortis         JP3171_for 1     22.92 75.5 27.6 13.32 11.66 14.35
fortis         SH520_for  1     21.86 71.3 23.5 12.6 10.36 12.05
fortis         JP3402_for 1     22.41 68 24.1 12.52 11.1 12.69
fortis         JP3539_for 2     22.36 68 24.3 12.35 10.28 11.43
scandens       JP3565_sca 1     22.39 68 21.8 14.31 8.44 8.81
fortis         JP3574_for 2     23.61 73 29.1 14.69 12.74 14.47
fortis         JP3582_for 1     21.11 65 16.4 10.04 9.55 9.43
scandens       JP3583_sca 1     20.85 67 20.5 15.1 8.04 8.49
scandens       JP3587_sca 2     21.65 61 20.7 14.7 7.9 7.81
magnirostris   JP3607_mag other 22.99 69 23 13.21 11.31 13.2

I've also tried this one: 

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.

Is it a problem with my phenotypic file?

plink association mapping vcf phenotype gwas
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updated by Sarthok • Sarthok • written by beausoleilmo beausoleilmo

1 answer

I have done similar analysis using plink 1.9. From your phenotype file as I can see in the sex column all values has to be numeric. If you are using a mac book to create the txt file please make sure you save (as) the file as UTF-8 (no BOM) because text file created in classic mac encoding does not work with plink.

If you please paste the analysis output message from plink I might be able to suggest you specific suggestions.

I have found Plink 1.9 forum very helpful.

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written by Sarthok • Sarthok

I ran od -c pheno1.txt on the terminal and saw that the end of line is only \n. I'm going to try it later. For the moment, I modified my R script to create my file like this: 

write.table(df.pheno,"~/Desktop/pheno1.txt", 
            quote = FALSE,
            col.names = TRUE,
            row.names = FALSE,
            eol = "\r\n"). # This is the line of code that I needed to write to add the \r\n!

I've also change the encoding with TextWrangler.

On the PLINK website, it's saying this http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml:

Sex (1=male; 2=female; other=unknown)

"If an individual's sex is unknown, then any character other than 1 or 2 can be used."

The message I have is this one (returning only a log file and a nose file, even if I have a sex column, and trying with the no BOM file...): 

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

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ run2.log ]
Analysis started:

 Thu Dec 29 12:48:31 2016

Options in effect:
    --noweb
    --file output_in_plink
    --pheno pheno1.txt
    --out run2

840907 (of 840907) markers to be included from [ output_in_plink.map ]
Warning, found 96 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ run2.nosex ]
96 individuals read from [ output_in_plink.ped ] 
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 96 missing
0 males, 0 females, and 96 of unspecified sex
Reading alternate phenotype from [ pheno1.txt ] 
0 individuals with non-missing alternate phenotype
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 96 missing
Before frequency and genotyping pruning, there are 840907 SNPs
96 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 840907 SNPs
After filtering, 0 cases, 0 controls and 96 missing
After filtering, 0 males, 0 females, and 96 of unspecified sex

Analysis finished: Thu Dec 29 12:49:38 2016
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written by beausoleilmo beausoleilmo

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