Edited the script to accept VCF files as input and adds more information...

to the output file. The VCF input can be in a directory or given individually to work with galaxy
Re-write it like a hash where you have 4 entries i.e

my %compl = ( 'T'=> 'A', 'A' => 'T' , 'G'=> 'C', 'C' => 'G');
return $compl{shift };