Sample and variant QC for exome cohort studies

This repository contains the code used for the QC of human exome cohorts

The code is written by members of Wellcome Sanger HGI group (https://www.sanger.ac.uk/group/human-genetics-informatics-hgi/) based on the gnomAD QC pipeline by Broad institute (https://github.com/broadinstitute/gnomad_qc/tree/main).

The current codebase has several branches — one for each dataset. The unification of branches and the code refactoring are in progress.

The howto for the code is here: https://hgi-projects.pages.internal.sanger.ac.uk/documentation/docs/how-to-guides/wes-qc-hail/

How to run the code and QC your data

The brief howto for the QC process is available in the WES-QC Hail howto.

The code is designed to run on the SPARK cluster with the Hail library installed. The manual for the cluster setting up is here.

How to get the latest changes from main

When working on an analysis branch, you can retrieve the latest changes from main by running:

make update

This will fetch the latest changes from main and rebase the current branch onto it. If there are any unstaged changes in the branch, you will be asked to commit or stash them first.

Developer's howto

How to run the tests and calculate coverage

The tests currently require running on the SPARK cluster. There are plans to make them runnable locally. They can be run by commands defined in Makefile.

To run all the tests:

make test

Or you can specify the type of test to run

make unit-test
make integration-test

To run the tests with coverage:

make unit-test-coverage
make integration-test-coverage

To run pre-commit hooks on commit

1. Install pre-commit

pip install pre-commit

2. pre-commit will automatically run on every commit
3. To run pre-commit manually on specific files

pre-commit run --files <file1> <file2>

4. mypy is configured to run manually because now it produces too many errors. To run it:

pre-commit run --hook-stage manual