remove --rm-dups argument

[ionox0]

for bcftools concat we are using all for the --rm-dups argument.

What was the original reasoning for using this?

We may have to use none . Otherwise, multliallelic positions (or multiple variants with same position), only one mutation is retained following vcf concatanation.

bcftools_params:
  allow_overlaps: true
  rm_dups: all # <--- here