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I have been able to get a working solution that produces my desired results... using set -x and the below modifications


if [[ $VCF = ${STRING } ]] # only execute file on match
then
...

I am using ubuntu 14.04 as my os.

/home/cmccabe/f1/file is the path to file (which has all the necessary information for the move, (folder name, ids).

The for loop on RDIR was for trimming...

I am trying to mv each of the .vcf files in the variants folder to the folder in /home/cmccabe/f2 that the .vcf id is found in file. $2 in file will always have the id of a .vcf in the variants...