📦 Request to Add Formula: SnpEff

[BenjaminDEMAILLE]

Hi Homebrew Science team,

I’d like to request the addition of a formula for SnpEff, a widely used variant annotation tool written in Java. It annotates and predicts the effects of genetic variants on genes and proteins, and is a commonly used alternative to Ensembl VEP.

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🔍 Tool Overview

• Name: snpeff
• Version: 5.2 (latest as of now)
• Source: https://github.com/pcingola/snpEff
• Website: https://pcingola.github.io/SnpEff/
• License: LGPL-3.0
• Platform: Cross-platform (Java-based)
• Languages: Java
• Distribution: Single .jar file + config files

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💡 Why it’s useful

SnpEff is a popular tool for:

• Annotating VCF files with gene, exon, codon, and protein effect information
• Predicting variant consequences (missense, frameshift, synonymous, etc.)
• Supporting many species and custom genome databases
• Fast and easy to integrate into variant calling pipelines

It’s especially useful when a lightweight alternative to VEP is desired, and is compatible with tools like GATK and bcftools.

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📦 Installation notes

SnpEff is distributed as a standalone .jar file with a set of supporting config files. It does not require compilation and works on any system with a Java runtime.

After installing the binary, users typically run:

snpeff download GRCh38.99
snpeff ann GRCh38.99 input.vcf > output.ann.vcf

✅ Proposed Formula

class Snpeff < Formula
  desc "Genetic variant annotation and effect prediction toolbox"
  homepage "https://pcingola.github.io/SnpEff/"
  url "https://github.com/pcingola/snpEff/archive/refs/tags/v5.2.tar.gz"
  sha256 "<insert_sha256_here>"
  license "LGPL-3.0-or-later"

  depends_on "openjdk"

  def install
    libexec.install Dir["*"]
    bin.write_jar_script libexec/"snpEff.jar", "snpeff"
  end

  def caveats
    <<~EOS
      To use SnpEff, you'll need to download genomic databases before annotation, e.g.:

        snpeff download GRCh38.105

      To annotate:

        snpeff ann GRCh38.105 input.vcf > output.vcf

      Documentation: https://pcingola.github.io/SnpEff/
    EOS
  end

  test do
    system "#{bin}/snpeff", "help"
  end
end

This formula installs snpeff as a simple wrapper around the snpEff.jar file, similar to how picard or gatk are installed in other ecosystems. The program can then be used as a CLI tool system-wide via the snpeff command.

Let me know if you'd prefer a snpSift companion formula to be submitted separately or as part of this one.

Thanks again for maintaining this excellent toolkit for the bioinformatics community!

Best regards