Try this:

use strict;
use warnings;
use Data::Dumper;

# Read files into an array and populate a hash
my($key1, $key2, %hash1, %hash2);

open (IN1,'<'.$ARGV[0]) || die "***can't open the file $!\n";

my $col1 = $ARGV[2];
my $col2 = $ARGV[3];

my @lines1 = <IN1>;
close IN1;
#$i=0;
#  Master
for (@lines1)
{
    chomp;
    
    my @a1 = split(/\t/, $_);
    
    my $key1 = $a1[$col1];
    
    $hash1{$key1} =$_

}

# check if key in file2 exists in file1 and if so merge the files
open (IN2,'<'.$ARGV[1]) || die "***can't open the file $!\n";


my @lines2 = <IN2>;
close IN2;

#open (OUT,'>'.$ARGV[2]) || die "***can't open the file $!\n";

# slave
for (@lines2)
{
    chomp;
    
    my @a2 = split(/\t/, $_);
    
    my ($key2) = $a2[$col2];
    $hash2{$key2} = $_;
    
    $hash1{$key2} = $hash2{$key2};
    

}


for my $key (sort keys %hash1)
{
    print "$hash1{$key}\n";
}
exit;
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