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/1.13 $ bcftools
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2 $ tar xf bcftools-1.13.tar.bz2 $ cd bcftools-1.13 # install a newer compiler from Red Hat software collections $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ $ scl enable devtoolset-7 bash $ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.13 --with-htslib=/export/apps/htslib/1.13 $ make $ sudo mkdir -p /export/apps/bcftools/1.13 $ sudo chown aorth /export/apps/bcftools/1.13 $ make install sudo chown -R root:root /export/apps/bcftools/1.13
This links bcftools against a system-wide installation of htslib/1.13.