myichorCNA

A simple python wrapper to run ichorCNA with a config file.

Getting started

1. Clone this repo

git clone https://github.com/matteolepur/myichorcna.git

2. cd into this repo and install myichorcna

pip install --editable .

3. Run ichorCNA on example data

myichorcna perform-inference --output-directory 'example/results' --ctdna-data-file 'example/ctdna.wig' --ichorcna-settings 'example/settings.yaml'

Quick documentation:

Inputs

Running ichorCNA requires two input files and an output location. An example of all the required files is given in the examples directory. A description of each required file is provided below:

1. --output-directory 'example/results': where to store all outputs from ichorCNA.
2. --ctdna-data-file 'example/ctdna.wig': path to .wig file containing all binned read counts outputted by readCounter.
3. --ichorcna-settings 'settings.yaml': path to .yaml file containing ichorCNA settings.

Example

We can run ichorCNA on the example data provided outputted to example/results:

myichorcna perform-inference --output-directory 'example/results' --ctdna-data-file 'example/ctdna.wig' --ichorcna-settings 'example/settings.yaml