├── .gitignore ├── 0_plink_extract.sh ├── 0_split_ld_reference.py ├── 1_find_overlaps.sh ├── 1b_filter_overlaps.py ├── 2_generate_manifest.py ├── 2b_filter_manifest.py ├── 3_make_commands.py ├── 3a_make_conditioning_commands.py ├── 3b_make_coloc_commands_opt.sh ├── 4_run_commands.sh ├── 5_combine_results.py ├── 6_process_results.py ├── 7_merge_previous_results.py ├── 8_copy_results_to_gcs.sh ├── Dockerfile ├── LICENSE ├── README.md ├── configs ├── config.yaml ├── grch38_chrom_lengths.tsv └── phenotype_id_gene_luts │ ├── HumanHT-12_V4_gene_metadata.tsv.gz │ └── Sun_pQTL_gene_metadata.tsv.gz ├── environment.yaml ├── filter_overlap_table.R ├── imputation_test ├── 1_download_inputs.sh ├── 2_calculate_ld.sh ├── 3_parse_ld.py ├── 4_create_features.py ├── 5_cross_validation.py ├── README.md └── scripts │ └── calc_ld_1000G.py ├── join_results_with_betas.py ├── other ├── 5b_filter_for_top_loci.py ├── count_coloc_rows.py ├── mean_time.py └── partition_json │ ├── process.py │ └── readme.md ├── partition_top_loci_by_chrom.py ├── run_coloc_pipeline_opt.sh ├── scripts ├── __init__.py ├── coloc_opt.R ├── coloc_opt.py ├── coloc_wrapper.py ├── concat_json.py ├── gcta.py ├── generate_overlap_table.py ├── partition_sumstats.py ├── select_relevant_sumstat.py └── utils.py └── setup.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/opentargets/genetics-colocalisation/HEAD/.gitignore -------------------------------------------------------------------------------- /0_plink_extract.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/opentargets/genetics-colocalisation/HEAD/0_plink_extract.sh -------------------------------------------------------------------------------- /0_split_ld_reference.py: -------------------------------------------------------------------------------- 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