I tried adding the F_MISSING tag using bcftools 1.16. When I run this command:

bcftools +fill-tags input.vcf.gz -- -t 'F_MISSING' | bcftools view -i 'INFO/F_MISSING<0.25' -Oz -o output.vcf.gz

I get the following error:

Error parsing "--tags F_MISSING": the tag "F_MISSING" is not supported

This command runs fine using bcftools 1.15. However, version 1.15 gives complications with other packages I use in my snakefile. Do you maybe know alternatives for how to add F_MISSING using bcftools 1.16 (if possible)?

When I type bcftools +fill-tags --version:

bcftools 1.9 using htslib 1.9
plugin at 1.9 using htslib 1.9

SOLUTION

Indeed the issue was that I was not installing the most recent version of Conda. I solved it by changing the .condarc file to solelely include the following lines:

channels:
    - conda-forge
    - bioconda
    - defaults

The order is crucial as well.