foreach my $line (@lines)
{
    my @chr_fields = grep {$_ =~ m/^chr/} split ("\t", $line)

    if (                                   # If...
      @chr_fields == 2                     # ...there are exactly two chr* fields...
      && $chr_fields[0] ne $chr_fields[1]  # ...which are not exactly the same...
    ) {
        print $w $line;
    }
}
close $w;