config.yaml

###
# Run-specific settings
# Adjust this section for each run.
###
gene_list: common/genes.csv
phenotype_list: common/phenotypeDescriptions.csv
rscript_path: Rscript
input_var_dir: input
occurance_cutoff: 10 # Variant occurance cut-off for categorical phenotypes
bootstrap_iterations: 1000

###
# Global settings
# Adjust this section only when using non-default inputs.
###
all_variants_path: ukb23148_c%s_b%s_v1_filtered_mut.csv
unique_variants_path: ukb23148_c%s_b%s_v1_all_weights.csv
withdraw_eids_path: common/withdraws.csv
variant_blocks_path: common/pvcf_blocks.txt
db_connect_path: db_connect.yaml
variant_predictors:
  VARITY: VARITY_R_LOO # Format: [predictor name]: [predictor column name in unique variants file]
  PolyPhen-2: Polyphen2_HVAR_score
  PROVEAN: PROVEAN_flipped
  SIFT: SIFT_flipped
  FATHMM: FATHMM_flipped
  MPC: MPC_score
  LRT: LRT_flipped
  REVEL: REVEL_score
  PrimateAI: PrimateAI_score
  CADD: CADD_raw
  DANN: DANN_score
  Eigen: Eigen-raw_coding
  GenoCanyon: GenoCanyon_score
  M-CAP: M-CAP_score
  MetaLR: MetaLR_score
  MetaSVM: MetaSVM_score
  MVP: MVP_score
  MutationTaster: MutationTaster_score
  SiPhy: SiPhy_29way_logOdds
  MutPred: MutPred_score
  EVE: EVE_score
plot_individual_correlations: false