VCF Format INFO field: why do some keys in it not appear in the documentation?

Question

[Matteo Schiavinato]

Hi all,

I have this doubt which I couldn't sort out by myself. I started working with VCF files since one month only, so it might be that it's just that I didn't stumble on the right piece of literature yet. My VCF lines in the file have an INFO field which is like this:

DP=20;VDB=0.000678823;SGB=-1.30291;MQ0F=0.5;AC=4;AN=4;DP4=0,0,19,0;MQ=3

Some of these Key=Value pairs are totally fine for me, the documentation is very clear. However, I can't find the description for all of them. For example: VDB, SGB, I don't know what they are.

Where can I find such information?

[WouterDeCoster]

Not sure if it's the case for all tools, but in a properly formatted vcf the explanation of the INFO field keys is in the header.

e.g. ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

Answer 1

[Pierre Lindenbaum]

you should find this information in the VCF header, in a INFO field

 grep '##INFO=<ID=VDB,' -m1  input.vcf

if it's missing: this is an error.