How to set up bcftools plugins?

Question

[Filago]

Hello,

I want to use the +fixref-plugin in BCFTOOLS. I already installed BCFTOOLS and used some "normal" commands. However when I want to use the +fixref command, the following issue arises:

No functional bcftools plugins were found. The environment variable BCFTOOLS_PLUGINS is not set
and no usable plugins were found in /usr/local/libexec/bcftools.

Do you know, how to solve this issue? Do I need to install fixref (how, from where...)?

Best,

Andreas

[4galaxy77]

When you compile bcftools you need to set a environmental variable export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins

[Pierre Lindenbaum]

the message said

The environment variable BCFTOOLS_PLUGINS is not set

did you set this BCFTOOLS_PLUGINS variable ? https://samtools.github.io/bcftools/howtos/plugins.html

Answer 1

[ATpoint]

Please confirm that you read: https://samtools.github.io/bcftools/howtos/plugins.html

There is a plugin subdirectory in the bcftools directory which you have to reference via the BCFTOOLS_PLUGINS env variable, so you either do something like:

export BCFTOOLS_PLUGINS='path/to/plugin_dir'

...each time before you run a command or put it into your .bashrc/.bash_profile.