Try to escape the curly braces:

`some_command a=\{1,2\},\{3,4\}`;
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Here is a complete example (on linux), using system instead of backticks to show the output:

$ cat foo.pl
#!/usr/bin/env perl

use strict;
use warnings;
system './some_command a=\{1,2\},\{3,4\}';
$
$ cat some_command
#!/usr/bin/env perl

use strict;
use warnings;
use Data::Dumper;
print Dumper(\@ARGV);
$
$ ./foo.pl
$VAR1 = [
          'a={1,2},{3,4}'
        ];
$
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