GWAS result too significant
Recently, I did some genome-wide association study employing PLINK1.9. However, when I analyze the result of association I found it too 'significant'. This must be false! My command is
~/Software/plink --vcf qz_beijing_wes.g.vcf.gz --snps-only --maf 0.001 --hwe 0.0001 --geno 0.1 --make-bed --out qz_beijing_wes
~/Software/plink --bfile qz_beijing_wes --assoc fisher --allow-no-sex --pheno pheno.txt --pheno-name CaseControl --out qz_beijing_wes_fisher
But the result shows too many p value less than 10^-20 !
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—assoc has been obsolete for many years. See https://www.cog-genomics.org/plink/2.0/assoc#glm for some discussion of how the “Eigenstrat” association analysis is performed with PLINK today.
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could you do a qq-plot ?
qqplot just like this