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 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.

Version: 0.1.16

Availability: GALILEO100

Target: all

Official web site:

Related Commands:

$ module load profile/bioinf

$ module load autoload vcftools

$ vcftools [ --vcf FILE | --gzvcf FILE | --bcf FILE] [ --out OUTPUT PREFIX ] [ FILTERING OPTIONS ] [ OUTPUT OPTIONS ]


$ module load profile/bioinf

$ module load autoload vcftools

$ vcftools --gzvcf input_file.vcf.gz --freq --chr 1 --out chr1_analysis

To see a list of alla available tools, run

 $ man vcftools

Or visit the Documentation page:


Help and Documentation:

You can find documentation on the system, with the command 'module help vcftools

- The manual is on the web at the original home page (/cineca/prod/build/applications/vcftools/0.1.15/gnu--10.2.0--gcc--8.3.1/BA_WORK/)


CINECA consultants can be reached through the address:'''

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