This hosts multiple scripts necessary for filtering and processing of variant calls in the vcfs/txt file generated by callers.
Project description
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:
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 section.
Usage
See CLI 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:
pip install poetry
Install Package Dependencies
Then install project dependencies with Poetry.
cd /path/to/postprocessing_variant_calls
poetry install .
Accessing Environment
To access the environment after initial setup up run:
poetry shell
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Source Distribution
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