How to run a GWAS in command line with Plink2?

How to run a GWAS in command line with Plink2?

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I am trying to run a GWAS in the command line with plink version 2, however when I run the following command plink2 –file hapmap1 I get the following error Error: Unrecognized flag (‘–file’)

I am trying to follow this tutorial zzz.bwh.harvard.edu/plink/tutorial.shtml#t6

Do I need to replace the file name in the command? (I have tried that but still get the same error)

I am unsure what to do as this is the first time I am using plink. I read somewhere that this command isnt compatible with plink2 but that was in 2017, so I am not sure how relevant that is now.


GWAS


PLINK

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