PLINK ASSOC : Skipping --assoc/--model since less than two phenotypes are present.

Question

[Michal Nevo]

Hello to all,

I have 10 vcf files - 5 female fish and 5 male fish I have merged all 10 fish to one vcf file.(all_fish.vcf) I want to do the plink association analysis on all 10 fish but I'm having a hard time.

I think that the problem is that temporary.fam does not recognize phenotypes..

my command:

plink --script assoc_command.txt

assoc_command.txt:

-noweb --const-fid --allow-extra-chr 0 --pheno pheno.txt --pheno-name Phenotype --vcf all_fish.vcf --assoc --out all_fish_assoc

my pheno.txt looks like that:

but...all_fish_assoc-temporary.fam looks like:

and the log:

Answer 1

[chrchang523]

The IIDs aren't identical between your two files.

[Michal Nevo]

I see now.. yes it was a stupid mistake but again..after changing it I get almost the same error.

[chrchang523]

See the first Warning in the log.

[Michal Nevo]

Thank you, it worked. I was not sure if it would produce sensible results if I will add this comment. Because after all, I have 5 females and 5 males.