remove --rm-dups argument

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
```