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>##

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>##

#! perl
use strict;
use warnings;

my $file1 = 'File_1b.txt';      # shift;
my $file2 = 'File_2b.txt';      # 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: $!";

chomp(my $header1 = <$in1>);
chomp(my $header2 = <$in2>);

my @heads1  = split /\s+/, $header1;
my @heads2  = split /\s+/, $header2;
my $low_idx = 5;
my %index_map;

for my $i ($low_idx .. $#heads1)
{
    $index_map{$i} = undef;
    my ($num1)     = $heads1[$i] =~ /^(\d+)/;
    next unless defined $num1;

    for my $j ($low_idx .. $#heads2)
    {
        my ($num2) = $heads2[$j] =~ /^(\d+)/;

        if (defined $num2 && $num1 == $num2)
        {
            $index_map{$i} = $j;
            last;
        }
    }
}

print $header1, "\n";

while (my $line1 = <$in1>)
{
    chomp $line1;
    my @fields1 = split /\s+/, $line1;

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

    chomp $line2;
    my @fields2 = split /\s+/, $line2;
    my @out     = @fields1;

    for my $i ($low_idx .. $#fields1)
    {
        my $j = $index_map{$i};

        if (       $fields1[$j] ne 'REF' &&
            exists $fields2[$j]          &&
                   $fields2[$j] ne 'REF')
        {
            if ($fields1[$j] eq $fields2[$j])
            {
                $out[$i] = 'REF';
            }
            else
            {
                $out[$i] = $fields2[$j];
            }
        }
    }

    print join(' ', @out), "\n";
}

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

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

##</code><code>##

23:33 >perl 959b_SoPW.pl
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

23:33 >