a b/kgwas/params.py 

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## The raw UKBB genotype data paths. If you have access to it, please modify the paths accordingly. 





  
  

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cohort_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/cohort/'





  
  

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ukbb_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/'





  
  

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main_data_path = '/dfs/project/datasets/20220524-ukbiobank/data/ukb_main/ukb52124.csv'





  
  

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kinship_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_rel_a79791_s488170.dat'





  
  

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withdraw_path = '/dfs/project/datasets/20220524-ukbiobank/data/withdraw'





  
  

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fam_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_lmdb_fam.csv'





  
  

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bim_path = '/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_lmdb_bim.csv'





  
  

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scdrs_traits = ['UKB_460K.mental_NEUROTICISM',





  
  

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 'PASS_FastingGlucose_Manning',





  
  

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 'PASS_Lupus',





  
  

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 'UKB_460K.biochemistry_HbA1c',





  
  

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 'PASS_ADHD_Demontis2018',





  
  

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 'UKB_460K.bmd_HEEL_TSCOREz',





  
  

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 'UKB_460K.disease_HYPOTHYROIDISM_SELF_REP',





  
  

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 'UKB_460K.blood_LYMPHOCYTE_COUNT',





  
  

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 'PASS_Insomnia_Jansen2019',





  
  

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 'UKB_460K.other_MORNINGPERSON',





  
  

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 'UKB_460K.cov_SMOKING_STATUS',





  
  

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 'UKB_460K.biochemistry_TotalBilirubin',





  
  

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 'PASS_BIP_Stahl2019',





  
  

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 'UKB_460K.biochemistry_HDLcholesterol',





  
  

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 'PASS_UC_deLange2017',





  
  

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 'UKB_460K.pigment_HAIR',





  
  

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 'UKB_460K.body_HEIGHTz',





  
  

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 'PASS_Worry_Nagel2018',





  
  

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 'PASS_Type_2_Diabetes',





  
  

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 'UKB_460K.body_BMIz',





  
  

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 'UKB_460K.disease_HYPERTENSION_DIAGNOSED',





  
  

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 'PASS_Primary_biliary_cirrhosis',





  
  

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 'UKB_460K.blood_RED_COUNT',





  
  

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 'UKB_460K.disease_CARDIOVASCULAR',





  
  

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 'PASS_DrinksPerWeek_Liu2019',





  
  

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 'PASS_SWB',





  
  

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 'PASS_VerbalNumericReasoning_Davies2018',





  
  

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 'UKB_460K.biochemistry_AlkalinePhosphatase',





  
  

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 'UKB_460K.bp_DIASTOLICadjMEDz',





  
  

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 'UKB_460K.disease_RESPIRATORY_ENT',





  
  

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 'UKB_460K.biochemistry_Cholesterol',





  
  

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 'PASS_Alzheimers_Jansen2019',





  
  

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 'UKB_460K.repro_NumberChildrenEverBorn_Pooled',





  
  

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 'UKB_460K.biochemistry_Triglycerides',





  
  

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 'UKB_460K.body_BALDING1',





  
  

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 'PASS_Coronary_Artery_Disease',





  
  

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 'UKB_460K.blood_PLATELET_COUNT',





  
  

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 'PASS_Multiple_sclerosis',





  
  

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 'UKB_460K.disease_AID_ALL',





  
  

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 'UKB_460K.repro_MENOPAUSE_AGE',





  
  

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 'PASS_Type_1_Diabetes',





  
  

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 'UKB_460K.lung_FVCzSMOKE',





  
  

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 'UKB_460K.blood_EOSINOPHIL_COUNT',





  
  

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 'UKB_460K.cancer_BREAST',





  
  

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 'UKB_460K.repro_MENARCHE_AGE',





  
  

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 'PASS_Intelligence_SavageJansen2018',





  
  

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 'PASS_ReactionTime_Davies2018',





  
  

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 'UKB_460K.biochemistry_SHBG',





  
  

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 'UKB_460K.blood_WHITE_COUNT',





  
  

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 'PASS_AtrialFibrillation_Nielsen2018',





  
  

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 'UKB_460K.blood_MONOCYTE_COUNT',





  
  

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 'UKB_460K.biochemistry_LDLdirect',





  
  

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 'UKB_460K.biochemistry_TotalProtein',





  
  

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 'UKB_460K.blood_MEAN_CORPUSCULAR_HEMOGLOBIN',





  
  

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 'UKB_460K.cov_EDU_COLLEGE',





  
  

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 'UKB_460K.body_WHRadjBMIz',





  
  

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 'PASS_IBD_deLange2017',





  
  

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 'PASS_SleepDuration_Dashti2019',





  
  

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 'PASS_BIP_Mullins2021',





  
  

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 'UKB_460K.cov_EDU_YEARS',





  
  

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 'UKB_460K.bp_SYSTOLICadjMEDz',





  
  

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 'UKB_460K.disease_ALLERGY_ECZEMA_DIAGNOSED',





  
  

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 'UKB_460K.disease_ASTHMA_DIAGNOSED',





  
  

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 'PASS_Schizophrenia_Pardinas2018',





  
  

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 'PASS_Rheumatoid_Arthritis',





  
  

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 'UKB_460K.lung_FEV1FVCzSMOKE',





  
  

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 'PASS_Celiac',





  
  

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 'UKB_460K.biochemistry_Glucose',





  
  

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 'PASS_MDD_Howard2019',





  
  

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 'PASS_GeneralRiskTolerance_KarlssonLinner2019',





  
  

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 'PASS_CD_deLange2017',





  
  

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 'UKB_460K.biochemistry_Testosterone_Male',





  
  

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 'UKB_460K.blood_RBC_DISTRIB_WIDTH',





  
  

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 'UKB_460K.impedance_BASAL_METABOLIC_RATEz',





  
  

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 'UKB_460K.biochemistry_AlanineAminotransferase']