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.