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.
See versions of bcftools which are available:
$ module avail bcftools
Load one version into your environment and run it:
$ module load bcftools/1.17 $ bcftools
Notes from the sysadmin during installation:
$ cd /tmp/ $ wget https://github.com/samtools/bcftools/releases/download/1.17/bcftools-1.17.tar.bz2 $ cd bcftools-1.17 $ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.17 --with-htslib=/export/apps/htslib/1.17 $ make $ sudo mkdir -p /export/apps/bcftools/1.17 $ sudo chown aorth:aorth /export/apps/bcftools/1.17 $ make install $ sudo chown -R root:root /export/apps/bcftools/1.17
This links bcftools against a system-wide installation of htslib/1.17.