VCFTools

Introduction

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 version of VCFTools is 0.1.14.

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

There is only one version of VCFTools installed at the moment, if there should be more than one you would have to specify the right version to load:

module load VCFTools/0.1.14

Always remember: this command is case sensitive!

After loading the module, you can use the program with

bcftools <command> <argument>

Documentation

The official documentation of VCFTools can be found here.