How I can run this code on my files?
$f in your command is not pointing anywhere since your for loop was defined as for file in *.vcf;. You should use $file instead of $f.

EDIT AS THE OP HAS EDITED THE QUESTION:

First of all, please copy and paste the error messages you are getting when seeking answers from the community, most of the time the error messages are clear enough to point to the right direction.

In you case, the problem is that you are trying to use a variable that you did not declare in the first place. It is explained above in my original answer but here I go again:

With this bit for file in *.vcf;, you are creating a variable file that you will using throughout the iteration. But then within the iteration, the next line (... -operation gx,r,f,f,f "$f" &gt; ..., you try to use another variable file, that has not been declared yet (as far as I can see from your code bit).