Entering edit mode
7.2 years ago
emyli
▴
10
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.
Check the first line on your VCF - what's the version?
Firstline says ##fileformat=VCFv4.2
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.