Metadata-Version: 2.4
Name: denovowest
Version: 0.1.1
Summary: A de novo mutation simulation framework
Author: Joanna Kaplanis, Kaitlin Samocha
Author-email: Erwan Delage <ed11@sanger.ac.uk>
License: MIT License
        
        Copyright (c) 2019 Genome Research Ltd.
        
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Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: gffutils
Requires-Dist: click
Requires-Dist: pyyaml
Requires-Dist: pysam
Requires-Dist: joblib
Dynamic: license-file

# 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](https://www.nature.com/articles/s41586-020-2832-5).  

`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](https://github.com/HurlesGroupSanger/DeNovoWEST/tree/v1.0.0)


## 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
```

