This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to install conda bcftools +fill-tags plugin ?

Hi,

I am very new to bioinformatics but I wanted to know is there a way to install bcftools +fill-tags plugin in conda env. Please consider that when I check my env there is not a bcftools folder and subsequently the plugin folder as instructed in the GitHub?

Any help is highly appreciated.

Thanks

bcftools
• 8,264 views • link
updated by Ram Ram • written by Daniel • Daniel

Conda command here.

conda create --name myenv  
conda activate myenv
conda install -c bioconda bcftools
• 0 views • link
written by MSRS MSRS

Thanks, I knew this and had been done! If you look at the question it says plugin more specifically +fill-tags. Any idea on that!

• 0 views • link
written by Daniel • Daniel

1 answer

Just poked around this myself, putting an answer for posterity. When installing from conda, the bcftools plugins are in $CONDA_PATH/envs/$ENV/libexec/bcftools so for me

BCFTOOLS_PLUGINS="${HOME}/miniconda3/envs/pysam/libexec/bcftools" bcftools plugin dosage

works like a charm.

• 0 views • link
written by LChart LChart

Log in to answer this question.

More posts like this