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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:

$ module load bcftools/1.11

Installation

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.

bcftools-software.txt · Last modified: 2021/02/21 09:50 by aorth