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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

pheno.txt:

enter image description here

log file: enter image description here

all_fish_assoc:

enter image description here

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?

a1 a2 snp assoc plink
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written by Michal Nevo • Michal Nevo

1 answer

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.

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written by Sam Sam

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

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written by Michal Nevo • Michal Nevo

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