PLINK ASSOC understanding the results
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
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?
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