Question: GWAS result too significant
0
gravatar for yehchan57
10 months ago by
yehchan5710
China
yehchan5710 wrote:

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 !

plink gwas genome • 255 views
ADD COMMENTlink modified 9 months ago by chrchang5237.3k • written 10 months ago by yehchan5710

could you do a qq-plot ?

ADD REPLYlink written 10 months ago by Nicolas Rosewick9.0k

qqplot just like this

ADD REPLYlink modified 9 months ago by RamRS30k • written 9 months ago by yehchan5710
1
gravatar for chrchang523
9 months ago by
chrchang5237.3k
United States
chrchang5237.3k wrote:

—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.

ADD COMMENTlink written 9 months ago by chrchang5237.3k
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