Metadata-Version: 2.1
Name: postprocessing_variant_calls
Version: 0.2.5
Summary: This hosts multiple scripts necessary for filtering and processing of variant calls in the vcfs/txt file generated by callers.
Home-page: https://cmo-ci.gitbook.io/postprocessing_variant_calls/
Author: Ronak Shah
Author-email: shahr2@mskcc.org
Requires-Python: >=3.8
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: PyVCF3
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: typer[all]
Project-URL: Repository, https://github.com/msk-access/postprocessing_variant_calls
Description-Content-Type: text/markdown

# Post-processing of variant calls

This package provides a variety of commands for manipulating different types of common outputs (e.g. mafs, vcf and txt files) from different bioinformatic variant callers such as mutect and vardict. 

Supported File Types:
- [maf](docs/MAF.md) 
- [vardict](docs/VARDICT.md)

# Installation  

For general use you can run: `pip install postprocessing_variant_calls`
or a tagged version with `pip install git+https://github.com/msk-access/postprocessing_variant_calls.git@<version>`

For setting up a development environment please see the [Setting up a Dev Environment](#Setting-up-a-Dev-Environment) section.

# Usage
See [CLI](docs/CLI.md) for commmand line usage of the package.

# Setting up a Dev Environment 
#### Install External Dependencies
Have an environment with python >= 3.8 installed. 

Install poetry: 

```bash
pip install poetry
```

#### Install Package Dependencies

Then install project dependencies with Poetry.

```bash
cd /path/to/postprocessing_variant_calls
poetry install .
```

#### Accessing Environment

To access the environment after initial setup up run: 

```bash
poetry shell
```

