├── .gitignore ├── 1_make_tables.Snakefile ├── 2_calculate_LD_table.Snakefile ├── 3_make_overlap_table.Snakefile ├── LICENSE ├── README.md ├── configs ├── config.yaml └── gwascat_superpopulation_lut.curated.v2.tsv ├── environment.yaml ├── master.bsub.sh ├── master.gcloud.sh ├── notebooks └── locus_overlap.ipynb ├── scripts ├── annotate_gwascat_varaintids.py ├── calc_ld_1000G.v2.py ├── calculate_locus_set_overlaps.py ├── cluster_gwas_catalog_associations.py ├── common │ └── utils.py ├── create_ld_input_table.py ├── extract_from_variant-index.py ├── format_finemapping_table.py ├── format_gwas_assoc.py ├── format_ld_table.py ├── format_overlap_table.py ├── format_sumstat_toploci_assoc.py ├── get_therapeutic_areas.py ├── make_FINNGEN_study_table.py ├── make_UKB_study_table.py ├── make_disease_mapping_lut.py ├── make_gwas_cat_study_table.py ├── merge_study_tables.py ├── merge_top_loci_tables.py ├── parquet_writer.py ├── process_ld.py └── study_table_to_parquet.py ├── setup_gcloud.sh ├── snakefiles ├── finemapping_table.Snakefile ├── ld_table_1.Snakefile ├── ld_table_2.Snakefile └── study_and_top_loci_tables.Snakefile └── tests ├── compare_postgap_to_plink_ld ├── 1_get_input_data.sh └── 2_compare_datasets.py └── temp_ld_parquet_fix ├── download.sh └── format_ld_table.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/opentargets/genetics-v2d-data/HEAD/.gitignore -------------------------------------------------------------------------------- /1_make_tables.Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/opentargets/genetics-v2d-data/HEAD/1_make_tables.Snakefile -------------------------------------------------------------------------------- /2_calculate_LD_table.Snakefile: -------------------------------------------------------------------------------- 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