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SnpEff Specifications

Process Details

  • Name: SnpEff
  • Process UUID: qGRU49XeIqEB5Hud6ABxMF5pCWfQYT
  • Process Group: gatk4

Overview

SnpEff is a variant annotation process that predicts the functional effects of genetic variants (SNPs, insertions, deletions) on genes and proteins. This process takes VCF files containing variant calls and provides comprehensive annotations including impact predictions, gene annotations, and functional classifications to help researchers understand the biological significance of genomic variants.

This process is implemented in Bash, which invokes the SnpEff Java application for variant effect prediction and annotation.

Key Functionality

  • Variant Effect Prediction: Predicts the functional impact of variants on genes, transcripts, and proteins
  • Comprehensive Annotation: Adds detailed annotations including gene names, transcript IDs, amino acid changes, and functional classifications
  • Impact Assessment: Classifies variants by predicted impact (HIGH, MODERATE, LOW, MODIFIER)
  • Statistical Summary: Generates HTML reports with variant statistics and distribution summaries
  • Gene-Level Analysis: Produces gene-level summaries of variant effects and impacts

Input/Output Specification

Inputs

Required Inputs

  • VCF Set
    • Description: Set of Variant Call Format files containing genetic variants to be annotated
    • Format: VCF

Outputs

  • Annotated VCF File

    • Description: VCF file with comprehensive variant annotations and effect predictions added to the INFO field
    • Format: VCF

  • Summary HTML Report

    • Description: Interactive HTML report containing variant statistics, impact distributions, and annotation summaries
    • Format: HTML

  • Gene Summary File

    • Description: Tab-delimited text file with gene-level variant statistics and impact summaries
    • Format: TXT

References & Resources

  • Tool Documentation: Contact the team for details on SnpEff configuration and database setup
  • Related Papers: Cingolani, P., et al. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2), 80-92.