Question: What does ALT 0 mean in a VCF?
0
gravatar for emyli
2.2 years ago by
emyli10
emyli10 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 2.2 years ago by finswimmer12k • written 2.2 years ago by emyli10

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

ADD REPLYlink written 2.2 years ago by RamRS24k

Firstline says ##fileformat=VCFv4.2

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by emyli10

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 2.2 years ago by RamRS24k
2
gravatar for finswimmer
2.2 years ago by
finswimmer12k
Germany
finswimmer12k 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 2.2 years ago • written 2.2 years ago by finswimmer12k

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 2.2 years ago by emyli10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1815 users visited in the last hour