--covar Plink Genome wide association

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5.4 years ago

uskhan.khan5 • 0

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 covar GWAS • 1.8k views

ADD COMMENT • link updated 5.4 years ago by finswimmer 16k • written 5.4 years ago by uskhan.khan5 • 0

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

How To Get Started Learning Gwas Analysis

ADD REPLY • link 5.4 years ago by zx8754 11k

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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 REPLY • link 5.4 years ago by uskhan.khan5 • 0

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