would like to know whether it is working or not.
Only you know if your code is working the way you want it to work. I don't follow your description of your requirements. That being said, the following looks suspicious: 
        my ($id, $sum, $haploStr) = split ('\t',$_);
        push @{$data{$id}{$sum}}, \$haploStr;

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Your data structure is a hash of hashes of ... scalar references. Did you really want a hash of hashes of arrays? 
        my ($id, $sum, @haploStr) = split ('\t',$_);
        push @{$data{$id}{$sum}}, \@haploStr;

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Use Data::Dumper after your while loop to get a better idea of what I'm taking about: 
print Dumper(\%data);

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I am using "undef" to remove the pattern which is matching (while iterating -- which I think is not good way of programing,
I agree that using undef seems unconventional here. Perhaps you want to delete?

In reply to Re: Extract the common values in hash of array with double keys by toolic
in thread Extract the common values in hash of array with double keys by snape

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