bcftools

BCFtools implements utilities for variant calling (in conjunction with SAMtools) and manipulating VCF and BCF files. The program is intended to replace the Perl-based tools from vcftools.

• Latest Version: 1.22
• Added: September, 2015
• Updated: December, 2025
• Link: https://samtools.github.io/bcftools

See versions of bcftools which are available:

$ module avail bcftools

Load one version into your environment and run it:

$ module load bcftools/1.22
$ bcftools

Notes from the sysadmin during installation:

$ cd /tmp/
$ wget https://github.com/samtools/bcftools/releases/download/1.22/bcftools-1.22.tar.bz2
$ cd bcftools-1.22
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.22 --with-htslib=/export/apps/htslib/1.22.1
$ make
$ sudo mkdir -p /export/apps/bcftools/1.22
$ sudo chown aorth:aorth /export/apps/bcftools/1.22
$ make install
$ sudo chown -R root:root /export/apps/bcftools/1.22

This links bcftools against a system-wide installation of htslib/1.22.