finemap_inputs.json

{
    "finemap.zones": "europe-west1-b europe-west1-c europe-west1-d",
    "finemap.docker": "eu.gcr.io/finngen-refinery-dev/finemap-suite:aa4f598",
    "finemap.sumstats_pattern": "gs://finngen-production-library-green/finngen_R7/finngen_R7_analysis_data/summary_stats/release/finngen_R7_{PHENO}.gz",
    "finemap.phenolistfile": "gs://r7_data/finemap/demopheno/conf/extended_demopheno",
    "finemap.phenotypes": "gs://r7_data/pheno/R7_COV_PHENO_V2.txt.gz",
    "finemap.preprocess.cpu": 1,
    "finemap.preprocess.mem": 52,
    "finemap.preprocess.rsid_col": "",
    "finemap.preprocess.chromosome_col": "#chrom",
    "finemap.preprocess.position_col": "pos",
    "finemap.preprocess.allele1_col": "ref",
    "finemap.preprocess.allele2_col": "alt",
    "finemap.preprocess.freq_col": "af_alt",
    "finemap.preprocess.beta_col": "beta",
    "finemap.preprocess.se_col": "sebeta",
    "finemap.preprocess.p_col": "pval",
    "finemap.preprocess.delimiter": "TAB",
    "finemap.preprocess.scale_se_by_pval": false,
    "finemap.preprocess.x_chromosome": true,
    "finemap.preprocess.set_variant_id": true,
    "finemap.preprocess.window": 1500000,
    "finemap.preprocess.max_region_width": 6000000,
    "finemap.preprocess.window_shrink_ratio": 0.9,
    "finemap.set_variant_id_map_chr":"23=X",
    "finemap.preprocess.p_threshold": 0.00000005,
    "finemap.ldstore_finemap.ldstore.sample": "gs://r7_data/R7_321464_samples.sample",
    "finemap.ldstore_finemap.ldstore.bgen_pattern": "gs://r7_data/bgen/chrom/finngen_R7_{CHR}.bgen",
    "finemap.ldstore_finemap.ldstore.cpu": 16,
    "finemap.ldstore_finemap.ldstore.mem": 96,
    "finemap.ldstore_finemap.ldstore.enable_fuse": false,
    "finemap.ldstore_finemap.n_causal_snps": 10,
    "finemap.ldstore_finemap.finemap.cpu": 8,
    "finemap.ldstore_finemap.finemap.mem": 52,
    "finemap.ldstore_finemap.susie.min_cs_corr": 0,
    "finemap.ldstore_finemap.susie.docker": "eu.gcr.io/finngen-refinery-dev/susie:0.11.92.2360607",
    "finemap.ldstore_finemap.susie.cpu": 8,
    "finemap.ldstore_finemap.susie.mem": 208,
    "finemap.ldstore_finemap.combine.cpu": 1,
    "finemap.ldstore_finemap.combine.mem": 7,
    "finemap.ldstore_finemap.filter_and_summarize.good_cred_r2": 0.25,
    "finemap.ldstore_finemap.filter_and_summarize.snp_annot_file":"gs://r7_data/annotations/R7_annotated_variants_v0.gz",
    "finemap.ldstore_finemap.filter_and_summarize.snp_annot_file_tbi":"gs://r7_data/annotations/R7_annotated_variants_v0.gz.tbi",
    "finemap.ldstore_finemap.filter_and_summarize.snp_annotation_fields":"most_severe,gene_most_severe",
    "finemap.ldstore_finemap.filter_and_summarize.cpu":1,
    "finemap.ldstore_finemap.filter_and_summarize.mem":2
}