PLINK basic command line usage

Question

[Dhara Awasthi]

Hey, I am new to PLINK. I want to carry out GWAS analysis on HapMapdata. I have downloaded all the scripts available and following the tutorial on https://github.com/MareesAT/GWA_tutorial/

How do I run the 1_Main_script_QC_GWAS.txt script in plink???

Also, I have placed PLINK in the directory 1_QC_GWAS. I am typing the command:

plink --bfile HapMap_3_r3_1.bed --missing

I am getting the error:

plink: unknown option "--file"
plink: unknown option "--missing"

Please help me!!!

[seta]

Please just use HapMap_3_r3_1 for the file name.

Also, it is required to add "--mind N" and "--geno N" after the --missing flag to check missingness per individual and Missingness per marker, respectively. The individuals or marker will be removed based on the missing rate threshold that you can determine (N)