First, your output is not exactly a CSV (comma separated value) format.

Second You would probably better off storing your metadata keys in an array rather than a hash, because an array preserves the order of the data (and not a hash).

Third, a regex might be simpler than a split if you just want to remove the trailing comma: 

while (my $line = <I1>) {
    chomp $line;
    if ($line =~ /##INFO=<ID=/) { 
        $line =~ s/,$//;
        # ...
}

[download]
Fourth, I do not see any \t in tour input.

Fifth, reading the file twice does not seem to be a very good idea. Can't you decide, based on the content, that you have finished reading the metadata and started to read the data?

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

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