Another variant annotator that leverages the ExAC server to annotate ones vcf.

Caveats

This has only been tested on FreeBayes output for two triploid samples.

It only works on the human genome assembley GR37 as that is all ExAC support. Also their version of VEP, which performs the annotations for the impact of the variant is rather outdated.

There isn't much required in terms of pre-requistes, besides an internet connection. The script does support the use of snpEff, however one must already have a local copy of the software installed. This can be found here https://pcingola.github.io/SnpEff

clone the repo to your local machine cd into the directory of the cloned repo and install with: pip3 install . -r requirements.txt

Limited unit testing has been made for this code using a combination of the hypothesis library to perform property-based testing and Contracts.

Example command to run the test:

pytest /path_to_repo/src/tests

• py3.8 - python
• pandas - python library for data manipulation
• hypothesis - python library for generating test data
• dpcontracts - python library for setting contracts

No verision software is used at this time

A simple tool to annotate one's vcf.

Example command to run the annotator script with all annotation functions:

navann --vcf ~/example/Challenge_data.vcf --verbose --outpath /path/to/outfolder/Challenge_data.ann.vcf --all

Run the annotator script, but output a csv with the fields of interest:

navann --vcf ~/example/Challenge_data.vcf --verbose --outpath /path/to/outfolder/Challenge_data.ann.vcf --all --simple_output /path/to/outfolder/Challenge_data.ann.csv

• Andrei Rajkovic - Initial work

This project is licensed under the MIT License - see the LICENSE.md file for details