File 1
CHROM	POS	REF	ALT	VARIANT_LIST	209T-D  459T-D	644T-D	94T-D	99T1-D	99T2-D	99T3-D	99T4-D	99T5-D	
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', 'A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'T']
...

##</code><code>##

File 2 
CHROM     POS     REF     ALT     VARIANT_LIST	209H-D	459H-D	644H-D	94H-D	99H-D	
['MT', '1010', 'G', 'A', 'A', 'REF', 'REF', 'REF', 'REF', 'REF']
['MT', '2962', 'C', 'T', 'T', 'REF', 'REF', 'T', 'REF', 'T']
....

##</code><code>##

 
CHROM	POS	REF	ALT	VARIANT_LIST	209T-D  459T-D	644T-D	94T-D	99T1-D	99T2-D	99T3-D	99T4-D	99T5-D	
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', 'A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'REF, 'T', 'REF', 'REF', 'REF', 'REF', 'REF']

##</code><code>##

#!/usr/local/bin/perl 
use strict;
use warnings;

my $file1 = shift;
my $file2 = shift;

open(my $in1, '<', $file1)
    or die "Cannot open file '$file1' for reading: $!";

open(my $in2, '<', $file2)
    or die "Cannot open file '$file2' for reading: $!";

my $header1 = <$in1>;
<$in2>;
my @heads1  = split "\t", $header1;
my $index = 5;
my %index_map;

for (@heads1)
{
    $index_map{$index++} = $1 + 4 if m/^(\d+)/;
}

print $header1;
while (my $line1 = <$in1>)
{
    my @fields1 = get_fields($line1);

    defined(my $line2 = <$in2>)
        or die "Data missing in file '$file2': $!";

    my @fields2 = get_fields($line2);
    my @out     = @fields1;

 for my $i (5 .. $#fields1)
    {
	my $j = $index_map{$i};
        
	if ($fields1[$i] ne 'REF')
            {
		
    		$out[$i] = $fields2[$j] if exists $fields2[$j] &&
						$fields2[$j] ne 'REF';

	    }

}
    @out = map { "'$_'" } @out;
    print '[', join(', ', @out), "]\n";
}

close $in2
    or die "Cannot close file '$file2': $!";

close $in1
    or die "Cannot close file '$file1': $!";

sub get_fields
{
    my ($line) = @_;

    chomp $line;
    my @fields = split "\t", $line;
    s{ ^ \[? ' }{}x for @fields;
    s{ ' \]? $ }{}x for @fields;

    return @fields;
}

##</code><code>##

CHROM	POS	REF	ALT	VARIANT_LIST	209T-D  459T-D	644T-D	94T-D	99T1-D	99T2-D	99T3-D	99T4-D	99T5-D	
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', 'A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'T']
...