├── .github ├── CODEOWNERS ├── dependabot.yml ├── pull_request_template.md ├── release.yml └── workflows │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .pydocstylerc ├── .pylintrc ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docker_files └── Dockerfile_VEP105 ├── docs ├── .gitignore ├── README.md ├── _static │ └── theme_overrides.css ├── build.sh ├── conf.py ├── directives.py ├── examples │ ├── index.rst │ └── vep.rst ├── generate_api_reference.py ├── getting_started.rst ├── index.rst ├── requirements.docs.in ├── requirements.docs.txt └── resource_sources.rst ├── gnomad ├── assessment │ ├── __init__.py │ ├── parse_validity_logs.py │ ├── summary_stats.py │ └── validity_checks.py ├── resources │ ├── __init__.py │ ├── config.py │ ├── grch37 │ │ ├── __init__.py │ │ ├── gnomad.py │ │ ├── gnomad_ld.py │ │ └── reference_data.py │ ├── grch38 │ │ ├── __init__.py │ │ ├── gnomad.py │ │ └── reference_data.py │ ├── import_resources.py │ └── resource_utils.py ├── sample_qc │ ├── __init__.py │ ├── ancestry.py │ ├── filtering.py │ ├── pipeline.py │ ├── platform.py │ ├── relatedness.py │ └── sex.py ├── utils │ ├── __init__.py │ ├── annotations.py │ ├── constraint.py │ ├── file_utils.py │ ├── filtering.py │ ├── gen_stats.py │ ├── intervals.py │ ├── liftover.py │ ├── parse.py │ ├── plotting.py │ ├── reference_genome.py │ ├── release.py │ ├── slack.py │ ├── sparse_mt.py │ ├── transcript_annotation.py │ ├── vcf.py │ └── vep.py └── variant_qc │ ├── __init__.py │ ├── evaluation.py │ ├── ld.py │ ├── pipeline.py │ ├── random_forest.py │ └── training.py ├── init_scripts ├── sparklyr-init.sh ├── vep101-init.sh ├── vep105-init.sh ├── vep81-init.sh └── vep85-init.sh ├── lint ├── pyproject.toml ├── pytest.ini ├── requirements-dev.in ├── requirements-dev.txt ├── requirements.txt ├── setup.py └── tests ├── assessment └── test_validity_checks.py ├── conftest.py ├── resources └── test_resource_utils.py ├── sample_qc └── test_de_novo.py └── utils ├── test_annotations.py ├── test_parse.py ├── test_sparse_mt.py ├── test_transcript_annotation.py └── test_vep.py /.github/CODEOWNERS: -------------------------------------------------------------------------------- 1 | * @broadinstitute/gnomad-production 2 | -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/gnomad_methods/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/gnomad_methods/HEAD/.github/pull_request_template.md -------------------------------------------------------------------------------- /.github/release.yml: 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