LICENSE
README.md
pyproject.toml
setup.py
joint_calling/__init__.py
joint_calling/_version.py
joint_calling/dataproc.py
joint_calling/filter_cutoffs.yaml
joint_calling/joint_genotyping.py
joint_calling/sample_qc.py
joint_calling/sm_utils.py
joint_calling/upload_processor.py
joint_calling/utils.py
joint_calling/vep-config.json
joint_calling.egg-info/PKG-INFO
joint_calling.egg-info/SOURCES.txt
joint_calling.egg-info/dependency_links.txt
joint_calling.egg-info/not-zip-safe
joint_calling.egg-info/top_level.txt
joint_calling/__pycache__/__init__.cpython-36.pyc
joint_calling/__pycache__/__init__.cpython-37.pyc
joint_calling/__pycache__/__init__.cpython-39.pyc
joint_calling/__pycache__/_version.cpython-37.pyc
joint_calling/__pycache__/utils.cpython-37.pyc
scripts/__pycache__
scripts/ancestry_pca.py
scripts/ancestry_plot.py
scripts/combine_gvcfs.py
scripts/create_rf_annotations.py
scripts/evaluation.py
scripts/final_filter.py
scripts/generate_freq_data.py
scripts/generate_info_ht.py
scripts/generate_variant_qc_annotations.py
scripts/load_vqsr.py
scripts/make_finalised_mt.py
scripts/mt_to_vcf.py
scripts/process_uploads.py
scripts/random_forest.py
scripts/sample_qc_flag_related.py
scripts/sample_qc_hard_filters.py
scripts/sample_qc_pcrelate.py
scripts/sample_qc_regressed_filters.py
scripts/sample_qc_subset_mt_for_pca.py
scripts/sample_qc_write_metadata.py
scripts/variant_qc_plotting.py
test/test_rf_evaluation.py
test/test_upload_processor.py