What operating system are you using for this exercise?

It seems that the text description of your problem says that everything you need to find the files to be moved and the locations to which they should be moved is found in a file named /home/cmccabe/f1/file, but your script is treating that regular file as a directory. What am I missing?

Furthermore, you go to a lot of work to create a variable named VCF which contains the name of a file after stripping off the .vcf filename extension. But when you start moving the .vcf files, you use $VCF as the name of those files without reinstating the filename extension???

I then got completely lost when you started a loop on all of the R_2019* files in $DIR. Note that the DIR variable is never defined in your script and is never mentioned in your description of what you are trying to do.

I'm having a hard time guessing at what files are being processed by the code:

Code:

 FILE2=$(awk '{print $2}' $f')

(which should have "$f" instead of $f). I'm guessing that this will set FILE2 to a list of filenames that you are then treating as a single filename; but since I don't know what the contents are of the file that has been selected by $f; I'm lost.

I'm assuming that you have tried running your script and it is failing to work. What diagnostics is it printing, or if there aren't any, in what way is it failing to do what you want it to do?

Please indent your code to show its structure. Then comments like "end if" and "end loop" won't be needed and we won't have to wonder where the start of the "if" and "loop" are located. I know the shell doesn't care about indentation, but you are a human and you're asking humans on this forum to read your code. Lack of indentation makes it make difficult for humans (including you) to understand what your code is trying to do.