Bcftools 1.16 able to add F_MISSING tag? - snakemake

Question

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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?
I installed bcftools1.16 in a newly created conda env using conda install -c bioconda bcftools as indicated on https://anaconda.org/bioconda/bcftools
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.

Answer 1

I'm only giving a partial answer here:
However, version 1.15 gives complications with other packages I use in my snakefile.
You could work around this by making snakemake use a dedicated conda environment for the rule(s) needing bcftools 1.15. E.g.:
rule fill_tags:
input:
...
output:
...
conda:
"envs/bcftools-1.15.yaml"
shell:
r"""
bcftools +fill-tags {input.vcf} -- -t 'F_MISSING' \
| bcftools view -i 'INFO/F_MISSING<0.25' -Oz -o {output.vcf}
"""
Where envs/bcftools-1.15.yaml contains something like:
dependencies:
- bcftools=1.15
then run snakemake with flag --use-conda