Question

Hi all, I've just written a tool adding one or more extra column in a VCF file. 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

Answer 1

Which kind of information do you want to add? I don't think that the VCF specifications allow to add new columns, but since this format is still in an early phase of development, you could contact the authors and propose them a new functionality.

However, VCF files should be used only to describe the SNPs and their genotypes, and any other kind of information should go somewhere else... for example, if you have statistics associated with a snp, you should consider a flat file or a database.

Answer 2

BEDTools now supports VCF and you can tack on any number of columns you want. That said, if you are looking for specific functionality within VCFTools, then this isn't helpful at all.