Establish windows of 10kb and calculate the average Recomb Rate
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What does the "kb" refer to in this instance?    10,000 bits?    10,000 bytes?    10,000 bogons?

my @recomb_all = @{get_contents ($recomb_all)};

...

sub get_contents {
...
    return (\@contents);
}    # ----------  end of subroutine get_contents  ----------
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Why return a reference to @contents to dereference it to copy to @recomb_all and not just copy it:

my @recomb_all = get_contents ($recomb_all);

...

sub get_contents {
...
    return @contents;
}    # ----------  end of subroutine get_contents  ----------
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my $length = (scalar @recomb_all) - 1;
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$length is not actually the "length" of any thing, you are using it as the last index of the array @recomb_all, which could more simply be written as $#recomb_all or -1.

        @{$contents[$x]} = split /\s+/;
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There is no need for an $x variable there:

        push @contents, [ split ];
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