Hi all,
I've just written a tool adding one or more **extra column** in a [VCF file](http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3). The header now looks like this:

	(...)
	#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    MY_COL1    MY_COL2    FORMAT    NA00001    NA00002    NA00003
	(...)

Is there something in the **VCF** spec saying that another column can't be added ?
because when I used **VCFTOOLS**, it says:

	vcftools --vcf file.vcf 
	(...)
	Scanning file.vcf ... 
	Ninth Header entry should be FORMAT: MY_COL1
	Currently scanning CHROM: 19
	Currently scanning CHROM: 20
	Currently scanning CHROM: X
Instead of inserting new columns which will screw up most tools, you should add your custom information at the **ANNO** column. This is what that field is designed for. With perl, it is very easy to extract the key-value pair there, e.g.:

	perl -ane 'print "MYKEY=$1\n" if $F[7]=~/MYKEY=([^;]+)/'

Furthermore, VCF is not only used for SNPs, but also for INDELs and SVs. To make this format, various people from several major sequencing centers have joined the discussion. In my opinion, it is quite stable now. Small details may be changed in future, but not the number of columns.