manhattan and QQ plot

[ahmed abdo]

Dear Christopher,

I perform GWAS using PLINK 2.

I use --covar, --qq-plot, --linear and -- adjust, then I will have .adjusted file that can be used for QQ plot.

For manhattan plot I need .linear file, but when I add -- adjust, the .linear file contain repeated SNPs information. It does not contain the overall information for each SNP such as position, chr, pval, etc.

Even without -- adjust, then .linear file still same.

How I can get both files to generate qq and manhattan plots?

I use --covar because I have covariates.

Thanks in advance for your help

[Christopher Chang]

It sounds like you are using PLINK 1.9.  With PLINK 2.0, you can control the columns that appear in the .adjusted file; see https://www.cog-genomics.org/plink/2.0/general_usage#colset and https://www.cog-genomics.org/plink/2.0/formats#adjusted .

[ahmed abdo]

Thanks so much. That was really helpful .