vcftools ☆
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Description:
Tools for working with VCF files
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Developer tools
Tags: bioinformatics genomics vcf genetics data-analysis
Install: brew install vcftools
About:
VCFtools is a comprehensive suite of utilities for working with Variant Call Format (VCF) files, the standard for storing genetic sequence variations. It provides a robust command-line interface for filtering, summarizing, and converting VCF data, making it essential for processing high-throughput sequencing data. The toolset supports both Perl and C++ implementations, offering flexibility for various bioinformatics workflows.
Key Features:
  • Efficiently filter and subset VCF files based on variant properties
  • Generate detailed statistics and reports on variant data
  • Convert between VCF and other genetic data formats
  • Perform basic population genetics analyses
Use Cases:
  • Quality control filtering of genomic variants from sequencing pipelines
  • Extracting specific variant subsets for candidate gene analysis
  • Generating summary statistics for population genetics studies
Alternatives:
  • bcftools – Part of the SAMtools suite, often faster for simple operations but VCFtools offers a wider range of specialized statistical functions.
  • SnpEff – Focuses on variant annotation rather than filtering and statistics, often used in conjunction with VCFtools.
Version History
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