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VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

This toolset can be used to perform the following operations on VCF files:

  • Filter out specific variants
  • Compare files
  • Summarize variants
  • Convert to different file types
  • Validate and merge files
  • Create intersections and subsets of variants

VCFtools consists of two parts, a perl module and a binary executable. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines.

Installed version

The currently installed versions of VCFTools are ...

  • VCFtools/0.1.14 on hpc-uniol-env
  • VCFtools/0.1.15-intel-2017a-Perl-5.26.0 on hpc-uniol-new-env
  • VCFtools/0.1.16-GCC-8.3.0 on hpc-env/8.3

Using VCFtools

If you want to find out more about VCFtools on the HPC cluster, you can use the command

module spider vcftools

This will show you basic informations e.g. a short description and the currently installed version.

To load the module, use the command

module load VCFtools

To load a specific version of VCFtools, you might need to change the environment and call for the specific version with module load

module load hpc-env/8.3
module load VCFTools/0.1.16

Always remember: this command is case sensitive!


The official documentation of VCFTools can be found here.