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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 bcftls 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.

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    $\begingroup$ Wait, what is version 1.9? Aren't you using version 1.16? $\endgroup$
    – terdon ♦
    Commented Nov 21, 2022 at 14:32
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    $\begingroup$ I know, I am pretty confused by that myself. I installed bcftools in a newly created conda env using conda install -c bioconda bcftools as indicated on anaconda.org/bioconda/bcftools and conda says v1.16 $\endgroup$
    – ra23mik
    Commented Nov 21, 2022 at 14:36
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    $\begingroup$ Conda might, but are you running the version installed in conda or the one on your system? Don't you need something like conda run bcftools --version? $\endgroup$
    – terdon ♦
    Commented Nov 21, 2022 at 14:38
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    $\begingroup$ I ran the following: conda activate bcftools1.16 and then conda list --show-channel-urls. Just to check again the version of bcftools: # Name Version Build Channel bcftools 1.9 h68d8f2e_9 bioconda $\endgroup$
    – ra23mik
    Commented Nov 21, 2022 at 14:41
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    $\begingroup$ Please put all of this into the question. I don't know much about conda, but it still looks like you're running the system-wide one. What's the output of type -a bcftools and, type -a bcftools | grep -v aliased | grep -oP '/\S+' | while read c; do echo "=== $c ==="; $c --version; done? $\endgroup$
    – terdon ♦
    Commented Nov 21, 2022 at 15:56

1 Answer 1

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$\begingroup$

The issue was that not installing the most recent version of Conda. It was solved by changing the .condarc file to solely include the following lines:

channels:
    - conda-forge
    - bioconda
    - defaults

The order is crucial as well.

Converted to answer from question.

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