denovowest 0.1.1

A de novo mutation simulation framework

DeNovoWEST

DeNovoWEST is a simulation-based method to test for a statistically significant enrichment of damaging de novo mutations (DNMs) in individual genes. This method scores all classes of variants (e.g. nonsense, missense, splice site) on a unified severity scale based on the empirically-estimated positive predictive value of being pathogenic, and incorporates a gene-based weighting derived from the deficit of protein truncating variants in the general population.

More information on the method can be found in Kaplanis, Samocha, Wiel, Zhang et al Nature 2020.

DeNovoWEST version 2.0.0 is a refactoring of the tool that, among other things, includes all the preleminary steps necessary before running the simulation analysis. It is built around nextflow and uses a modular approach to accomodate for each user's specific goal. The version used for publication can be found here

Requirements

To run DeNovoWEST 2.0.0, you need to have conda and nextflow installed.

Install

git clone https://github.com/HurlesGroupSanger/DeNovoWEST.git
git checkout develop
conda create -f misc/conda/denovowest.yml

Run

All the parameters are provided via a configuration file that has to be tuned to your own analysis.

cd nextflow
nextflow run denovowest.nf -c nextflow.config.annotate