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:
$ module load bcftools/1.11
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2 $ tar xf bcftools-1.11.tar.bz2 $ cd bcftools-1.11 $ ./configure --prefix=/export/apps/bcftools/1.11 --with-htslib=/export/apps/htslib/1.11 $ make $ sudo mkdir -p /export/apps/bcftools/1.11 $ sudo chown aorth /export/apps/bcftools/1.11 $ make install $ sudo chown -R root:root /export/apps/bcftools/1.11
This links bcftools against a system-wide installation of htslib/1.11.