# Store the contents of the first file into $hash{col1_col2}

open (FILE1, $filename1) or die "Unable to open $filename1 because $!\n";
while ($line = <FILE1>) {
    chomp ($line);
    ($chrX, $chrpos, $value1, $value2) = split (/\t/, $line);
    $key1 = join ("_", $chrX, $chrpos);
    $hash{$key1}++;
};
close FILE1;