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 routine.