How to use plugin commands in bcftools?

Question

My goal is to use bcftools to check that the reference alleles in my dataset (vcf file) match with a reference genome (fasta file) using the fixref plugin.

Working on command line, I first set the following environment:

export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins

The following code is recommended for test datasets with mismatches:

bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m top

When I run this code using my own files (please note that my data is .vcf, not .bcf) I get the following error:

[main] Unrecognized command

If I simply enter:

bcftools

I get a list of the only 5 commands (view, index, cat, ld, ldpair) that I can use. So although I've set the environment, does it somehow need to be activated? Do I need to run my command through a bash script?

Answer 1

bcftools

was pointing to a deprecated version of bcftools (0.1.19) in ../bin/, while

BCFTOOLS_PLUGINS=/path/to/bcftools/plugins

was pointing to the plugins for bcftools version 1.10.2 outside /bin/

Replacing ../bin/bcftools (0.1.19 with 1.10.2) was the fix.