A set of tools written in Perl and C++ for working with VCF files.

Welcome to VCFtools

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:

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.


To obtain VCFtools, please visit the downloads page.

Variant call format specification

VCFtools is compatible with VCF versions 4.0, 4.1 and 4.2. For more information regarding the VCF format, please visit the VCF specification page.


For help regarding VCFtools or the VCF format, please see the mailing lists.

Citations and Licensing

Information about licensing and publications can be found here.


Other useful links can be found on this page.