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:

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.