test_dataset_s3.yaml

#please do not skip any of the options from this template, if needed set to None as they might be referenced in the code
pheno_prefix: embedGEM_toy_data
sumstat_dirs:
  - s3://2023-embedgem/toy_data/sumstats/pheno1/
  - s3://2023-embedgem/toy_data/sumstats/pheno2/
s3_output_path: s3://<output path here>
bfile_template: s3://2023-embedgem/toy_data/bfiles/emb_toy_chr{CHROM}
chromosomes: #defaults to all chromosomes
  - "1"
  - "2"
  - "3"
  - "4"

heritability_eval:
  pval_thresh: 1.0e-3 # default to 5e-8
  max_p: 1.0e-1 # default to 5e-8

clumping:
  maf_threshold: 0.0001 # default 0.0001
  max_kb: 250 # default 250
  max_pval_all_variants: 0.05 # default 1e-5
  max_pval_lead_variants: 1.0e-3 # 5e-8
  min_r2: 0.5 # default 0.5

disease_relevance_options:
  disease_relevance_bfile_template: s3://2023-embedgem/toy_data/bfiles/emb_toy_chr{CHROM}
  pheno_file: s3://2023-embedgem/toy_data/test_pheno.tsv
  covar_file: s3://2023-embedgem/toy_data/test_cov.tsv
  pheno_id_col: eid
  cov_id_col: eid
  cov_cols: ['sex']
  pheno_type: continuous
  pheno_col: labels
  pheno_sep: '\t'
  cov_sep: '\t'
  boot_reps: 2000 #default 2000