One way is to collect the rs things in an array (@samples) and the AW things in a hash-of-arrays inside your nested for-loops, then print it all out after the loops. UNTESTED:

my @samples;
my %aws;

foreach my $geno( @ {$genotype} ){
  push @samples, $geno->[4];
  if(defined $geno->[3]){
    push @{ $aws{$geno->[1]} }, $geno->[3];

  }#end of if loop to check the genotype defined
  else{
    push @{ $aws{$geno->[1]} }, 'NO';

  }

}#end of @$genotype


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