Hi.

I made vcf files using UnifiedGenotyper in GATK and found that many of mutants had 1/2 at genotype (GT) field. 

As I understand, 0/0 = homo ref, 0/1 = hetero, 1/1 = homo alt.

Does anyone know what exactly 1/2 mean?

Thank you!
just to expand Devon's answer, which is perfectly correct...

this is due to a VCF format constrain, which states that 0 must always be the reference allele. this doesn't mean that the reference allele must be in a particular sample, it just means that a particular base is used as reference by a scientific community agreement.

in case you're working with human samples, this agreement is now supported by the Genome Reference Consortium, and I really hope that when the time comes (we shouldn't be that far) they'll be able to build a consensus reference based on entire world populations allele frequencies, but meanwhile we have to stick to the current reference. current GRCh38 [has already done][1] some work in this direction though.

since humans are diploids, sequencing a particular position will give you a pair of alleles, and usually the reference will be 1 of that 2 alleles. but this is not always the case, and you may find (as you already did) that a particular position doesn't contain the reference allele. this is rare, but far from being impossible due to the lack of population genetics evidences in the reference selected, as explained previously.


  [1]: https://www.biostars.org/p/94826/