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
• vardict

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

Contributing to Documentation

The Gitbook for this repository is configured so changes are written in Gitbook and synced with the docs branch.

To contribute to the documentation, you can write your changes in Gitbook, request a review, and merge the changes. Keep in mind, you will need access to the organization to contribute.

Each file-type supported should have a section in the Gitbook detailing the implementation of the file-type and a justification of it's operations. For example, the maf file-type has it's own section, which includes a description of how a maf is defined internally in the package and a justification of it's operations and how to use them.

Beyond file-type sections, you will also notice a section called cli, which lists all commands in the postprocessing_variant_calls package. Do not manually edit this section. This section is created using the typer-cli package, which uses the typer help parameters specified in typer commands to generate documentation. It is automatically updated by the git-action, .github/workflows/document_package.yml upon a push to the main branch. To make sure the cli.md document updates to include newly added commands, specify all relevant typer help parameters.

If you'd like to see a mock of your typer commands as they'll appear in the cli.md document, you can run: poetry run typer postprocessing_variant_calls.main utils docs > docs/cli.md in a properly configured dev environment. Note that this file should not be included in your PRs. The cli.md should be only updated through the git-action, .github/workflows/document_package.yml.