Question: What does ALT 0 mean in a VCF?
0
gravatar for emyli
21 months ago by
emyli0
emyli0 wrote:

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.

ADD COMMENTlink modified 21 months ago by finswimmer11k • written 21 months ago by emyli0

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

ADD REPLYlink written 21 months ago by RamRS22k

Firstline says ##fileformat=VCFv4.2

ADD REPLYlink modified 21 months ago • written 21 months ago by emyli0

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.

ADD REPLYlink written 21 months ago by RamRS22k
2
gravatar for finswimmer
21 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

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

ADD COMMENTlink modified 21 months ago • written 21 months ago by finswimmer11k

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).

ADD REPLYlink written 21 months ago by emyli0
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