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snpeff_annotation-nf

Nextflow DSL2 pipeline to annotate VCF files with SnpEff and dbSnp

This repository contains a Nextflow DSL2 pipeline for annotating genetic variants in VCF files using SnpEff and dbSnp database. The pipeline processes input VCF files, performs various annotations, and generates a comprehensive annotation file.

Prerequisites

Make sure you have the following dependencies installed before running the pipeline:

Pipeline Overview

  1. FilterInputFiles: Filters input VCF files using PLINK 2 to retain PASS variants with a maximum of 2 alleles.

  2. AnnotateWithRSID: Annotates variants with RSID using SnpSift and the dbSNP database.

  3. AnnotateWithImpact: Annotates variants with functional impact using snpEff and a specified reference genome.

  4. FullyAnnotateWithDbSNP: Performs comprehensive annotation using SnpSift and dbNSFP database, including information on gene impact, gnomAD data, REVEL scores, ClinVar information, and more.

  5. ExtractFields: Extracts relevant fields from the annotated VCF files and creates a tab-separated text file with a header for downstream analysis.

Usage

  1. Clone the repository:

    git clone https://github.com/IARCbioinfo/snpeff_annotation-nf
cd snpeff_annotation-nf

  2. Adjust the nextflow.config file if necessary. The package versions are specified in environment.yml file.

  3. Run the pipeline with:

    nextflow run main.nf -profile conda

Input

Name Default value Description
--input_folder_with_VCF_files ${baseDir}/VCFs/ Folder containing *vcf.gz files

Parameters

  • Optional

Name Default value Description
--reference_genome GRCh37.75 Reference genome
--dbNSF_path ${baseDir}/dbNSFP4.1a.txt.gz dbNSFP database
--dbSNP_path ${baseDir}/dbsnp150.vcf.gz dbSNP database
--output_path ${baseDir}/output Output folder

Output

The final annotated and extracted information will be available in the output directory as full_annotation.txt.

Customization

  • Adjust the memory requirements etc in the nextflow.config file.
  • Customize the annotation processes in the main.nf script based on your specific requirements.

Acknowledgments

  • This pipeline utilizes various bioinformatics tools and databases, including PLINK, bcftools, SnpSift, snpEff, dbNSFP, and dbSNP.