PLINK ASSOC understanding the results

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 performed the plink association analysis on all 10 fish with the command:

-noweb --const-fid --allow-no-sex --allow-extra-chr --pheno pheno.txt --pheno-name Phenotype --vcf all_fish.vcf --assoc --out all_fish_assoc

pheno.txt:

log file:

all_fish_assoc:

but I'm not sure why the SNP column is a dot and what is the meaning of the A1 A2 . Is A1 -Minor allele name in Male fish? and A2 in Female?

Answer 1

[Sam]

A1 is the effective allele and A2 the non-effective allele.

SNP column is a dot likely because in your VCF file, there isn't a SNP ID, so PLINK use ., which is the default.

[Michal Nevo]

Thank you! Do you know how can I add SNP ID to my VCF?