You could create a Hash-of-Arrays data structure. The hash keys could be a concatenation of the 1st 3 columns, and the hash values could be an array of all the last column values: 
use strict;
use warnings;

my %data;
while (<DATA>) {
    my @cols = split;
    my $col3 = pop @cols;
    my $key = "@cols";
    push @{ $data{$key} }, $col3;
}

for (keys %data) {
    print "$_ ", join(',', @{ $data{$_} }), "\n";
}

__DATA__
chr1 12345 34567 gene1 
chr1 12345 34567 gene2

[download]

Output: 

chr1 12345 34567 gene1,gene2

[download]

In reply to Re: Duplicate removal by toolic
in thread Duplicate removal by perl_paduan

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