vt normalize fails to report on reference inconsistency #124
Description
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 <[email protected]>
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.