Bcftools consensus when reference is a deletion

Question

[selplat21]

Hello,

I am trying to call a consensus on a VCF file like so:

bcftools consensus species.vcf.gz -f Reference.fasta --absent N > Consensus.fasta

Error: The site SUPER_1:173197 overlaps with another variant, skipping...

I looked at this site and included the previous site

SUPER_1 173196  .       AT      A      
SUPER_1 173197  .       T       A   

How would you recommend dealing with this overlapping variant error:

I have tried bcftools norm -m +any, but this does not modify these types of sites in the VCF, so am unsure how to merge these types of entries or call a consensus without these overlapping variant errors.