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bcftools-software

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

Usage

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

Installation

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.

bcftools-software.txt · Last modified: 2021/09/05 10:51 by aorth