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:
The IIDs aren't identical between your two files.
I see now.. yes it was a stupid mistake but again..after changing it I get almost the same error.
See the first Warning in the log.
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.
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