Try 
#!perl
use strict;
use Text::CSV;

my %info=();
my $line_count=0;
while (my $line = <DATA>){
  chomp($line);
  if ($line =~ /##INFO=<ID=([^,]+)/){
    $info{$1}=[];
  } else {
    my (undef,%hash) = split /[\t;=]/,$line;
    
    for (keys %info){
      push @{$info{$_}},$hash{$_} || 'NA';
    }
    ++$line_count;
  }
}

my $csv = Text::CSV->new ( {binary=>1, eol=>"\012"} )  
   or die "Cannot use CSV: ".Text::CSV->error_diag();
open my $fh,'>','output.csv' 
   or die "Could not open output.csv $!";

my @col_head = sort keys %info;
$csv->print($fh, \@col_head);
for my $i (1..$line_count){
  my @row = map { $info{$_}[$i-1] } @col_head;
  $csv->print($fh, \@row);
}

__DATA__
##INFO=<ID=AA,
##INFO=<ID=AB,
##INFO=<ID=AC,
1    AA=1;AB=2;AC=3
2    AA=2;AB=2
3    AA=5;AB=1;AC=1

[download]
poj

In reply to Re: Adding missing values into a hash by poj
in thread Adding missing values into a hash by Biopolete

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