Using WES model, deepvariant calls the following variant in the vcf file:
NC_000001.11 84574341 . CAGCAGCGCT C,T . . . GT:GQ:DP:AD:VAF:PL 1/0:3:97:25,45,26:0.463918,0.268041:36,0,47,0,16,44
For this variant, the genotype is 1/0, meaning that one allele is REF, and the other allele is C. What is confusing is that deepvariant also calls a T however this is not referenced anywhere in the GT field.
What is the point of calling T if it does not occur in the sample?