Question: --covar Plink Genome wide association
gravatar for uskhan.khan5
2.2 years ago by
uskhan.khan50 wrote:

I have a data in plink file formats, a covar file is a separate file and pheno file is also a separate file. i want to find an association in plink. anyone can tell me the basic steps for Genome-wide association?

snp plink covariance gwas covar • 973 views
ADD COMMENTlink modified 2.2 years ago by finswimmer14k • written 2.2 years ago by uskhan.khan50

Plink is very well documented, and has many tutorials online for GWAS. What have you tried so far?

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ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by zx87549.9k

I have tried QC and case-control association and now just want to include pheno and covariate for the association. Commands are not a problem but I don't know the basic steps for GWA. for example 1-basic summary statistics, 2- QC, 3- association. I am just confused that should I include .cov file as --pheno and then apply QC and then -- association then go for plotting graphs?

ADD REPLYlink written 2.2 years ago by uskhan.khan50
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