====== 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.

===== Information =====

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

===== Usage =====

See versions of bcftools which are available:
<code>$ module avail bcftools</code>

Load one version into your environment and run it:
<code>$ module load bcftools/1.22
$ bcftools</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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