SnpEffWrapper

Takes a VCF and infers annotations and variant effects from a GFF using SnpEff.

Notes for the version on this fork

It was forked from sanger-pathogens/SnpEffWrapper on October 2020 and adapted to answer a couple of personal analysis needs.

Easy install

A pre-built singularity container is available from SingularityHub and can easily be obtained on any maching that supports singularity containers by running:

singularity pull shub://afonsoguerra/SnpEffWrapper

Exclusive features compared to original

• Tested with python3
• setup.py was edited so it actually installs with pip
• The Java version check code was changed to match any openjdk version (realistic any recent version will work with SNPeff). Will probably complain if Oracle Java is used.
• the version of SNPeff in the dependencies script was updated (to v4_3t_core)
• the default command line of SNPeff in the wrapper was changed to match my personal needs. (I suggest you have a look at lines 231 and around on snpEffWrapper/wrapper.py to see if this matches your needs)
• changed code so it doesn't crash if variants don't have an annotation field
• the SNPeff summary CSV is produced and kept
• added a Singularity recipe file for easy deployment
• Added repo to SingularityHub

Content

• Introduction
• Installation
  • Running the tests
• Usage
  • Example usage
  • Alternative coding tables
  • Input
• License
• Feedback/Issues
• Citation

Introduction

SnpEff is a tool that annotates and predicts the effects of variants on genes. SnpEffWrapper takes a VCF and, using SnpEff, infers annotations and variation effects from a GFF. If you use SnpEffWrapper, please consider citing SnpEff. This software is not endorsed in any respect by the original authors.

Installation

SnpEffWrapper has the following dependencies:

• SnpEff (>= 4.1)
• Java (>= 1.7)
• Jinja2
• PyVCF
• PyYAML

Details for the installation are provided below. If you encounter an issue when installing SnpEffWrapper please contact your local system administrator. If you encounter a bug please log it here or email us at [email protected]

Install snpEff and Java 1.7 then

pip install git+https://github.com/sanger-pathogens/SnpEffWrapper.git

Running the tests

The test can be run from the top level directory:

./snpEffWrapper/tests/test_wrapper.py

Usage

$ snpEffBuildAndRun --help
usage: snpEffBuildAndRun [-h] [--snpeff-exec SNPEFF_EXEC]
                         [--java-exec JAVA_EXEC] [--coding-table CODING_TABLE]
                         [-o OUTPUT_VCF] [--debug] [--keep]
                         gff_file vcf_file

Takes a VCF and applies annotations from a GFF using SnpEff

positional arguments:
  gff_file              GFF with annotations including a reference genome
                        sequence
  vcf_file              VCF input to annotate (NB must be aligned to the
                        reference in your GFF

optional arguments:
  -h, --help            show this help message and exit
  --snpeff-exec SNPEFF_EXEC
                        Path to your prefered SnpEff executable (default:
                        snpEff.jar)
  --java-exec JAVA_EXEC
                        Path to Java 1.7 (default: java)
  --coding-table CODING_TABLE
                        A mapping of contig name to coding table formatted in
                        YAML
  -o OUTPUT_VCF, --output_vcf OUTPUT_VCF
                        Output for the annotated VCF (default: stdout)
  --debug               Show lots of SnpEff and other debug output
  --keep                Keep temporary files and databases (useful for
                        debugging)

• snpEffBuildAndRun will look for SnpEFF.jar in the following locations:
  • the file specified by --snpeff-exec
  • snpEff.jar in your local directory
  • snpEff.jar in your PATH
• SnpEff needs Java 1.7 to run; snpEffBuildAndRun will look in the following locations:
  • the file specified by --java-exec
  • java in your PATH

Example usage

$ snpEffBuildAndRun snpEffWrapper/tests/data/minimal.gff snpEffWrapper/tests/data/minimal.vcf -o minimal.annotated.vcf

Alternative coding tables

You can provide a coding table for each VCF contig otherwise it'll default to SnpEff's 'Bacterial_and_Plant_Plastid'. You can do this by providing a mapping for each contig in your VCF to the relevant table in snpEffWrapper/data/config.template in YAML format.

For example:

snpEffBuildAndRun minimal.gff minimal.vcf \
  --coding-table 'default: Standard'
  
snpEffBuildAndRun minimal.gff minimal.vcf \
  --coding-table '{CHROM1: Standard, MITO1: Mitochondrial}'
  
snpEffBuildAndRun minimal.gff minimal.vcf \
  --coding-table '{default: Standard, MITO1: Mitochondrial}'

NB you don't need curly brackets if you're only mapping one contig (or setting a default); you do need them if you're setting different coding tables.

Input

• The GFF must contain the reference sequence in Fasta format
• The VCF must be aligned against the reference in the GFF
• At least one of the contigs in the VCF must have annotation data in the GFF (you'll get warnings for each VCF config not in the GFF)
• You cannot provide unknown coding tables (i.e. that can't be found in config.template)

License

SnpEffWrapper is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page or email [email protected].

Citation

If you use this, please consider citing SnpEff. This software is not endorsed in any respect by the original authors.