by ProperSoft

VCFTools is a set of command-line tools for working with VCF files and performing genetic variant analysis.

Operating system: Windows

Publisher: ProperSoft

Release : VCFTools

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VCFTools is a software package for manipulating and analyzing genetic variation data in the form of VCF files. It is a powerful set of tools for working with VCF files, including filtering, merging, sorting, and various statistical operations. The software is written in C++ and is available as a source code package or as a pre-compiled executable.

VCFTools allows efficient analysis and manipulation of VCF files.

VCFTools is a comprehensive suite of tools for working with VCF files. It includes a wide range of features, such as:

• Filtering: VCFTools offers a range of filtering options, allowing users to select specific ranges of data, filter out samples with specific characteristics, and apply other criteria.

• Merging: VCFTools can merge multiple VCF files into a single file, allowing users to combine data from different sources.

• Sorting: VCFTools provides options for sorting VCF files by a variety of criteria, including sample ID, chromosome, and position.

• Statistical Analysis: VCFTools offers a range of statistical operations, such as calculating summary statistics, running tests of Hardy-Weinberg equilibrium, and computing population differentiation statistics.

• Visualization: VCFTools includes a visualization tool for plotting data from VCF files.

• Exporting: VCFTools can export data in a variety of formats, such as PLINK, PHASE, and FASTA.

• Compatibility: VCFTools is compatible with a wide range of software, including R, Perl, and Python.

• Documentation: The software includes comprehensive documentation, which includes tutorials and examples.

• Support: VCFTools provides a range of support options, including an online forum, mailing list, and developer support.


VCFTools is an excellent tool for working with VCF files. It is easy to use and provides a wide range of features, making it a great choice for anyone working with genetic variation data.
VCFTools requires a working Unix/Linux environment with a C++ compiler installed. It also requires the zlib library and the GNU scientific library (GSL). On some systems, the GNU Scientific Library may need to be installed separately.

Performs a wide range of manipulations and analyses on VCF files.
Open-source, allowing users to contribute to and improve its functionality.
Supports parallel processing for handling large data sets efficiently.

Limited file format compatibility restricts data processing options.
No graphical interface can make usage challenging for beginners.
Lacks extensive documentation for troubleshooting and learning.
image/svg+xmlBotttsPablo Stanley Körner Matthew Q.
VCFTools is a powerful software for processing and manipulating genetic data. It provides many useful functions, including filtering, merging and sorting. I had a great experience using it to analyze the genetic diversity of a population. VCFTools was easy to install and use, and the data processing was fast and efficient. The graphical user interface was also intuitive, making it simple to access the various features. I especially liked the ability to use different kinds of filters, and the customizable output options. However, I did find that the documentation was a bit confusing, so it took some time to figure out how to use all of the features.
image/svg+xmlBotttsPablo Stanley Körner Robert B.
VCFTools is a powerful software for analyzing genetic variation data. It offers a wide range of statistical analyses and visualization tools which can be used to explore the data in great detail. It is also easy to use and quite intuitive. The documentation is comprehensive and covers most of the tasks one may need to perform. Despite being a useful tool, sometimes the software can be slow to respond when dealing with large datasets.
image/svg+xmlBotttsPablo Stanley Körner Jay Cabaniss
VCFTools is a command-line tool for manipulating and analyzing Variant Call Format (VCF) files. It provides a variety of functions for filtering, merging, and summarizing VCF files, as well as calculating basic population genetic statistics such as allele frequency and heterozygosity. Additionally, it includes tools for performing basic quality control checks on VCF data, such as checking for missing data and calculating various measures of sample relatedness. Overall, VCFTools is a powerful and flexible tool for working with VCF files in genome-wide association studies and other genetic analyses.
image/svg+xmlBotttsPablo Stanley Körner Aiden S*********s
The software has a user-friendly interface and provides a wide range of useful tools for variant calling and filtering in genomic data analysis.
image/svg+xmlBotttsPablo Stanley Körner Kai
Reliable for variant data manipulation, could improve user interface.
image/svg+xmlBotttsPablo Stanley Körner Harrison
Reliable for genetic variant analysis.
Genetic data analysis tool, easy to use, lots of options.
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