LICENSE
README.md
pyproject.toml
setup.py
larcoh/__init__.py
larcoh/dataproc.py
larcoh/filetypes.py
larcoh/main.py
larcoh/pipeline.py
larcoh/targets.py
larcoh/utils.py
larcoh.egg-info/PKG-INFO
larcoh.egg-info/SOURCES.txt
larcoh.egg-info/dependency_links.txt
larcoh.egg-info/not-zip-safe
larcoh.egg-info/requires.txt
larcoh.egg-info/top_level.txt
scripts/ancestry_pca.py
scripts/ancestry_plot.py
scripts/annotate_as.py
scripts/check_pedigree.py
scripts/combine_gvcfs.py
scripts/create_rf_annotations.py
scripts/evaluation.py
scripts/final_filter.py
scripts/final_mt_to_vcf.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/make_noref_mt.py
scripts/make_subset_mt.py
scripts/random_forest.py
scripts/release_vcf_export_chrom.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_somalier_to_ht.py
scripts/sample_qc_subset_mt_for_pca.py
scripts/sample_qc_write_metadata.py
scripts/siteonly_ht_to_vcf.py
scripts/variant_qc_plotting.py
test/test_rf_evaluation.py
test/test_upload_processor.py