vt normalize fails to report on reference inconsistency

[ankjel]

I have been running vt normalize on vcfs containing at least one variant where REF does not correspond to the reference, without encountering any errors.
Based on the wiki and options, I would expect an error and I am now wondering if I misunderstood the documentation or if there is an issue with the version I am running.

Command:
vt normalize -r human_g1k_v37.fasta myfile.vcf -o myfile.normalized.vcf

Running in container heuermh/vt:latest

 vt --version
vt v0.5772-60f436c3
The MIT license
Copyright (c) 2013 Adrian Tan <atks@umich.edu>

Output:

options:     input VCF file                                  myfile.vcf
         [o] output VCF file                                 myfile.normalized.vcf
         [w] sorting window size                             10000
         [m] no fail on masked reference inconsistency       false
         [n] no fail on reference inconsistency              false
         [q] quiet                                           false
         [d] debug                                           false
         [r] reference FASTA file                            human_g1k_v37.fasta


stats: biallelic
          no. left trimmed                      : 0
          no. right trimmed                     : 0
          no. left and right trimmed            : 0
          no. right trimmed and left aligned    : 0
          no. left aligned                      : 0

       total no. biallelic normalized           : 0

       multiallelic
          no. left trimmed                      : 0
          no. right trimmed                     : 0
          no. left and right trimmed            : 0
          no. right trimmed and left aligned    : 0
          no. left aligned                      : 0

       total no. multiallelic normalized        : 0

       total no. variants normalized            : 0
       total no. variants observed              : 2
       total no. reference observed             : 0

The 0 count of "total no. reference observed" made me question if reference inconsistency is checked only for variants that are normalized, but I couldn't find this described anywhere.

Thanks for any input.

[ankjel]

It looks to me like vt normalized only checks reference alleles on variants that are being nomalized. I don't think this behaviour is described clearly in the documentstion (https://genome.sph.umich.edu/wiki/Vt#Normalization).