VEP-small_variant

A workflow for genomic small variant annotation using Ensembl VEP and the GRCh38 reference genome.

Overview

This repository contains scripts to automatically annotate VCF files, which includes preprocessing, batch submission to VEP, and final result aggregation.

Directory Structure

• VEP_script/: Core annotation logic and submission scripts.
• VEP_script/utils/: Helper functions and shared utilities.

Requirements

• Python 3.12.2
• BCFtools 1.18
• Anaconda3 23.3.1
• Ensembl VEP v115.1

Quick start

For detailed information regarding this annotation workflow, please refer to the VEP_script documentation

Example usage:

module load Python/3.12.2

cd VEP_script/
python 00_vep_batch_submitter.py /path/to/input/vcf/ /output/path/

Reference Genomes

The workflow automatically detects the chromosome naming convention and applies the appropriate reference during normalization:

• UCSC Style (with "chr" prefix): Uses Homo_sapiens_assembly38.fasta.
• Ensembl Style (without "chr" prefix): Uses Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz.

Customization: Changing Reference Genomes

If you need to use a different reference FASTA, you must manually update the REF_FASTA variable in 01_preprocess.sh.

Important

The script uses a conditional check to handle chromosome naming conventions (with or without the "chr" prefix). Ensure you update the correct path within the if-else block:

• With "chr" prefix: Update REF_FASTA inside the if block.
• Without "chr" prefix: Update REF_FASTA inside the else block.

Example in 01_preprocess.sh:

if [[ "$checkCHR" =~ ^chr ]]; then
    # Update this path for 'chr' prefixed VCFs
    REF_FASTA=/path/to/your/custom_hg38_with_chr.fasta
else
    # Update this path for non-'chr' prefixed VCFs
    REF_FASTA=/path/to/your/custom_GRCh38_no_chr.fa.gz
fi

Databases and plugins

Data in the VEP cache

• Ensembl database (VEP), version 115.1
• MANE, version 1.4

Plugins

• dbscSNV, version 1.1
• dbNSFP, version 4.9a
  • SIFT ensembl 66, released Jan, 2015
  • PROVEAN ensembl 66, version 1.1, released Jan, 2015
  • Polyphen-2, version 2.2.2, released Feb, 2012
  • LRT, released November, 2009
  • MutationTaster 2, data retrieved in 2015
  • MutationAssessor, release 3
  • FATHMM, version 2.3
  • fathmm-MKL
  • CADD, version 1.7
  • DANN
  • MetaSVM and MetaLR
  • M-CAP, version 1.3
  • GERP++
• SpliceAI SNV and indel, version 1.3
• LOEUF, based on gnomAD v2.1.1, liftover from GRCh37
• PrimateAI, version 0.2
• MaxEntScan
• DosageSensitivity
• satMutMPRA
• LoFtool
• pLI
• NMD

Custom datasets

• DVD, version 9.2
• ClinVar, released 20251109
• RepeatMasker, download from UCSC Table Browser, data last updated: 2022-10-18
• gnomAD exome, version 4.1
• gnomAD genome, version 4.1
• gnomAD genome coverage, version 3
• Taiwan Biobank SNV and indel, called by Jacob's lab
• Taiwan Biobank SNV and indel, released by Taiwan Biobank
• MitoMap
• Taiwan Biobank mitochondria SNV and indel, called by Jacob's lab
• gnomAD mitochondria, version 3.1