User Tools

Site Tools


This is an old revision of the document!


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
$ 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.1613901026.txt.gz · Last modified: 2021/02/21 09:50 by aorth