What does ALT 0 mean in a VCF?

Question

[emyli]

Hi,

I've recently come across variants in my VCF with the ALT allele 0, as in the 4th line of the example below. Can someone please explain what this nomenclature refers to?

Chr Start       End        Ref Alt
1   12885289    12885289    G   -
1   13036587    13036587    C   T
1   13696054    13696054    G   A
1   14105139    14105139    T   0

Thanks.

[Ram]

Check the first line on your VCF - what's the version?

[emyli]

Firstline says ##fileformat=VCFv4.2

[Ram]

Hmmm. VCFv4.2 should not have a 0 allele. v4.2 has a LOT of pain points but AFAIK ALT=0 isn't one of them.

Answer 1

[finswimmer]

Hello,

this doesn't look like a vcf file. It seems to be an input file for ANNOVAR. I don't know for what it is useful, but due to the manual, it seems that "0" means that there is no information about how the Alt looks like.

fin swimmer

[emyli]

Thanks, that is useful. This is actually generated from the ANNOVAR output .txt file (which I understand to be a more visually friendly version of the corressponding VCF).