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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/1.8

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2
$ tar xf bcftools-1.8.tar.bz2
$ cd bcftools-1.8
$ ./configure --prefix=/export/apps/bcftools/1.8 --with-htslib=/export/apps/htslib/1.8
$ make
$ sudo mkdir /export/apps/bcftools/1.8
$ sudo chown -R aorth:aorth /export/apps/bcftools/1.8
$ make install
$ sudo chown -R root:root /export/apps/bcftools/1.8

This links bcftools against a system-wide installation of htslib/1.8.

bcftools-software.txt · Last modified: 2018/06/01 22:17 by aorth