README.md
pyproject.toml
merit/__init__.py
merit/common.py
merit/constants.py
merit/errors.py
merit/stats.py
merit/coloc/__init__.py
merit/coloc/coloc_core.py
merit/coloc/coloc_sensitivity.py
merit/example_data/__init__.py
merit/example_data/downloads.py
merit/example_data/dummy_ipd_data.py
merit/example_data/dummy_summary_data.py
merit/example_data/examples.py
merit/example_data/example_datasets/1000Genomes_ALL.chrY.vcf.gz
merit/example_data/example_datasets/1000Genomes_ALL.chrY.vcf.gz.tbi
merit/example_data/example_datasets/1000Genomes_ALL.chrY_ld.txt
merit/example_data/example_datasets/coords_small.txt.gz
merit/example_data/example_datasets/covariance_mvmr_spiller.p
merit/example_data/example_datasets/formatdat_mvmr.tsv.gz
merit/example_data/example_datasets/ld_clump_b37.txt.gz
merit/example_data/example_datasets/ld_matrix_b37.txt.gz
merit/example_data/example_datasets/ld_matrix_b38.txt.gz
merit/example_data/example_datasets/merit.cnf
merit/example_data/example_datasets/prs.sample
merit/example_data/example_datasets/prs_chr01.bgen
merit/example_data/example_datasets/prs_chr01.bgen.bgi
merit/example_data/example_datasets/prs_chr01.vcf.gz
merit/example_data/example_datasets/prs_chr01.vcf.gz.tbi
merit/example_data/example_datasets/prs_chr19.bgen
merit/example_data/example_datasets/prs_chr19.bgen.bgi
merit/example_data/example_datasets/prs_chr19.vcf.gz
merit/example_data/example_datasets/prs_chr19.vcf.gz.tbi
merit/example_data/example_datasets/prs_chr22.bgen
merit/example_data/example_datasets/prs_chr22.bgen.bgi
merit/example_data/example_datasets/prs_chr22.vcf.gz
merit/example_data/example_datasets/prs_chr22.vcf.gz.tbi
merit/example_data/example_datasets/prs_gwas.txt.gz
merit/example_data/example_datasets/steiger_filtering.tsv.gz
merit/example_data/example_datasets/vars_liftover.txt.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr1.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr1.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr19.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr19.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr22.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/chr_hint/cohort_a_chr22.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_16143520_16143520.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_16143520_16143520.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_39402680_39402909.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_39402680_39402909.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_43030219_43036480.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr19_43030219_43036480.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr1_55496039_55496039.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr1_55496039_55496039.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr1_56945666_56996191.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr1_56945666_56996191.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr22_16050822_16050856.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr22_16050822_16050856.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr22_50000004_50000277.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_a/pos_hint/cohort_a_chr22_50000004_50000277.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr1.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr1.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr19.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr19.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr22.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/chr_hint/cohort_b_chr22.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_16143520_16143520.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_16143520_16143520.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_39402680_39402909.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_39402680_39402909.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_43030219_43036480.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr19_43030219_43036480.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr1_55496039_55496039.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr1_55496039_55496039.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr1_56945666_56996191.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr1_56945666_56996191.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr22_16050822_16050856.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr22_16050822_16050856.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr22_50000006_50000277.vcf.gz
merit/example_data/example_datasets/test_file_pools/cohort_b/pos_hint/cohort_b_chr22_50000006_50000277.vcf.gz.tbi
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr1.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr1.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr1.bgen.metadata2.mmm
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr1.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr19.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr19.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr19.bgen.metadata2.mmm
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr19.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr22.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr22.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr22.bgen.metadata2.mmm
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/cohort_c_chr22.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/create_bgen.sh
merit/example_data/example_datasets/test_file_pools/cohort_c/chr_hint/samples.txt
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_16143520_16143520.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_16143520_16143520.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_16143520_16143520.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_39402680_39402909.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_39402680_39402909.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_39402680_39402909.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_43030219_43036480.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_43030219_43036480.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr19_43030219_43036480.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_55496039_55496039.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_55496039_55496039.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_55496039_55496039.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_56945666_56996191.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_56945666_56996191.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr1_56945666_56996191.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_16050822_16050856.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_16050822_16050856.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_16050822_16050856.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_50000010_50000277.bgen
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_50000010_50000277.bgen.bgi
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/cohort_c_chr22_50000010_50000277.vcf
merit/example_data/example_datasets/test_file_pools/cohort_c/pos_hint/samples.txt
merit/gwas/__init__.py
merit/gwas/ingest.py
merit/gwas/site_list.py
merit/gwas/utils.py
merit/ipd/__init__.py
merit/ipd/admission.py
merit/ipd/common.py
merit/ipd/corr_factory.py
merit/ipd/corr_matrix.py
merit/ipd/dosage_cache.py
merit/ipd/files.py
merit/ipd/manifest.py
merit/ipd/regions.py
merit/ld/__init__.py
merit/ld/clumping.py
merit/ld/factory_clumping.py
merit/ld/handlers.py
merit/ld/variants.py
merit/misc/__init__.py
merit/misc/sojo.py
merit/misc/steiger_filtering.py
merit/mr/__init__.py
merit/mr/base.py
merit/mr/conmix.py
merit/mr/egger.py
merit/mr/ivw.py
merit/mr/median.py
merit/mr/mendelian_randomization.py
merit/mr/mode.py
merit/mr/mvmr.py
merit/mr/selection.py
merit/mr/utils.py
merit/mr/wald.py
merit/pipelines/__init__.py
merit/pipelines/_outcome_loader.py
merit/pipelines/assembly.py
merit/pipelines/assembly_precheck.py
merit/pipelines/coloc.py
merit/pipelines/columns.py
merit/pipelines/constants.py
merit/pipelines/extract.py
merit/pipelines/features.py
merit/pipelines/filtering.py
merit/pipelines/formatting.py
merit/pipelines/io.py
merit/pipelines/ld_reference.py
merit/pipelines/maf.py
merit/pipelines/mr.py
merit/pipelines/parameters.py
merit/pipelines/region_plan.py
merit/pipelines/result.py
merit/pipelines/sample_size.py
merit/pipelines/validation.py
merit/pipelines/cli/__init__.py
merit/pipelines/cli/_args.py
merit/pipelines/cli/_log.py
merit/pipelines/cli/_result.py
merit/pipelines/cli/run_coloc.py
merit/pipelines/cli/run_extract.py
merit/pipelines/cli/run_mr.py
merit/pipelines/cli/run_mr_hpc.py
merit/pipelines/cli/run_mr_parallel.py
merit/pipelines/data/__init__.py
merit/pipelines/data/human_chromosomes.PROVENANCE.md
merit/pipelines/data/human_chromosomes.tsv
merit/pipelines/data/methods.toml
merit/pipelines/hpc/__init__.py
merit/pipelines/hpc/jaf.py
merit/pipelines/hpc/planner.py
merit/pipelines/hpc/task_script.py
merit/pipelines/methods/__init__.py
merit/pipelines/methods/_config.py
merit/pipelines/methods/_protocol.py
merit/pipelines/methods/_registry.py
merit/pipelines/methods/_support.py
merit/pipelines/methods/egger.py
merit/pipelines/methods/ivw.py
merit/pipelines/methods/median.py
merit/pipelines/methods/mode.py
merit/pipelines/methods/mvmr.py
merit/pipelines/methods/wald.py
merit/pipelines/parallel/__init__.py
merit/pipelines/parallel/executor.py
merit/pipelines/parallel/options.py
merit/pipelines/parallel/publish.py
merit/pipelines/parallel/runtime.py
merit/pipelines/parallel/worker.py
merit_mr.egg-info/PKG-INFO
merit_mr.egg-info/SOURCES.txt
merit_mr.egg-info/dependency_links.txt
merit_mr.egg-info/entry_points.txt
merit_mr.egg-info/requires.txt
merit_mr.egg-info/top_level.txt
resources/conda/LICENSE
tests/test_ci_dependency_lock.py
tests/test_ci_image_config.py
tests/test_ci_locked_environment.py
tests/test_conda_recipe.py
tests/test_constants.py
tests/test_errors_formatting.py
tests/test_imports.py
tests/test_pypi_upload_script.py
tests/test_pyproject_metadata.py
tests/test_run_docker.py
tests/test_stats.py
tests/test_version_config.py