Hi

I was wondering about your answer and therefore made this selfcontained snippet which should show the relevant elements.

#!/bin/env perl
use strict;
use warnings;
use 5.010;

my %info;
while (my $line = <DATA>) {
    chomp $line;
    if ($line =~ /##INFO=<ID=/) {
        my ($first, $second) = split /,/, $line;
        my ($firstsecond, $secondsecond) = split /ID=/, $first;
        $info{$secondsecond}=();
    }
    elsif ($line !~ /#/) {
        my ($numbers, $data) = split /\s+/, $line;
        foreach my $dat ($data){
            my @elements = split /;/, $data;
            my %rowvalues;
            foreach my $element (@elements) {
                my ($key, $value) = split /=/, $element;
                $rowvalues{$key} = $value;
            }
            foreach my $key (keys %info) {
               if(exists $rowvalues{$key}) {
                   push @{$info{$key}}, $rowvalues{$key};
               }
               else {
                   push @{$info{$key}}, 'NA';
               }
            }
        }
    }
    else {
        next;
    }
}
foreach my $header (sort keys %info) {
    say $header, ' => ', join(',', @{$info{$header}});
}

__DATA__
# First the headers
##INFO=<ID=AA,
##INFO=<ID=AB,
##INFO=<ID=AC,
# then the data
1   AA=1;AB=2;AC=3
2   AA=2;AB=2
3   AA=5;AB=1;AC=1
[download]

I hope this will clarify what was said before. I change one split from '\t' to '\s+' because of pasting this code herein would probably destroy tghe tab character.

Regards
McA

Thank you very much. It works perfect :)