G'day xxArwaxx,

"any ideas if there is a BioPerl module that can do that, or how to approach this problem ?"

I'm not familiar with the BioPerl modules; however, based on your problem description, a script to achieve this is very straightforward:

#!/usr/bin/env perl -l

use strict;
use warnings;
use autodie;

use Text::CSV;

my $ref_file = 'pm_1079751_reference.csv';
my @gen_files = qw{pm_1079751_source1.gen pm_1079751_source2.gen};
my $allele_sep = '-';

my %ref_data;

my $ref_csv = Text::CSV::->new;
open my $ref_fh, '<', $ref_file;
while (my $row = $ref_csv->getline($ref_fh)) {
    $ref_data{$row->[0]} = join $allele_sep, @$row[1,2];
} 
close $ref_fh;

for my $gen_file (@gen_files) {
    my $gen_csv = Text::CSV::->new({allow_whitespace => 1});
    open my $gen_fh, '<', $gen_file;
    while (my $row = $gen_csv->getline($gen_fh)) {
        next unless exists $ref_data{$row->[2]};
        if ($ref_data{$row->[2]} eq join $allele_sep, @$row[3,4]) {
            print join(',' => @$row[2,3,4]),
                    "\n\tfound in '$gen_file':\n\t\t", join ', ' => @$
+row;
        }
    }
    close $gen_fh;
}
[download]

You stated the file you've already created is in CSV format, so I've used the Text::CSV module to parse it.

[Side note: CSV files have, by convention, a .csv extension, not a .txt extension (as you indicated you used).]

Your description of the .gen files seems to indicate a CSV format so I've used Text::CSV for these as well. If that's a false assumption on my part, you'll need to make some code changes; however, the logic I've used shouldn't need reworking.

Using these test files:

$ cat pm_1079751_reference.csv
34787638,A,C
34787800,A,G
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$ cat pm_1079751_source1.gen 
C1, M1, 99999999, A, C, ... source1 info ...
C1, M2, 34787638, A, G, ... source1 info ...
C1, M3, 34787800, A, C, ... source1 info ...
C1, M4, 34787800, A, G, ... source1 info ...
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$ cat pm_1079751_source2.gen 
C1, M1, 99999999, A, C, ... source2 info ...
C1, M2, 34787638, A, G, ... source2 info ...
C1, M4, 34787800, A, G, ... source2 info ...
C1, M3, 34787638, A, C, ... source2 info ...
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I get this output:

34787800,A,G
    found in 'pm_1079751_source1.gen':
        C1, M4, 34787800, A, G, ... source1 info ...
34787800,A,G
    found in 'pm_1079751_source2.gen':
        C1, M4, 34787800, A, G, ... source2 info ...
34787638,A,C
    found in 'pm_1079751_source2.gen':
        C1, M3, 34787638, A, C, ... source2 info ...
[download]