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:

• Nextflow
• conda
• dbSNP database
• dbNSFP database

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.