Unrecognized flag in Plink2

Question

[Abbas.M]

Hello all, I have been trying to calculate linkage disequilibrium on plink2 in linux, but it is constantly showing an error, following is my command and error

plink2 --file hapmap1 (this is the command that I typed)

PLINK v2.00a3LM 64-bit Intel (31 Aug 2020)     www.cog-genomics.org/plink/2.0/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink2.log.
Options in effect:
  --file hapmap1
Start time: Fri Sep 25 21:21:12 2020
Error: Unrecognized flag ('--file').
For more info, try "plink2 --help <flag name>" or "plink2 --help | more".
sam@biotechnology plinktutorial]$ plink2  --file hapmap1

Actually, this is a plink tutorial, and in this tutorial they have mentioned every command, and the input files are also in standard plink format. At first, I was trying to calculate LD on my own data that shows the same error i-e unrecogized flag. I thought there is a problem in my file or somewhere else in my command. Then i tried to use the tutorial data of plink and typed some command exactly same as given in the tutorial, but it is showing the same error on its own tutorial data. What i anticipated is that, is there any change in commands of plink for the latest version, that is plink2. I think some of the commands of older version of plink are not valid for latest version. Can anyone explain, why is it happening. Why is it showing this error?

Start time: Fri Sep 25 21:21:12 2020
Error: Unrecognized flag ('--file').

[Abbas.M]

I got it, thank you for your quick response

[GenoMax]

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Answer 1

[chrchang523]

plink 2.0 is still under development. Features which enable workflows that were previously impossible with plink have been prioritized over things that already work perfectly well in plink 1.9. You should use plink 1.9 for now.