Obtaining polygenic risk scores

Commands used to generate the best output (in Linux terminal):

Rscript PRSice/PRSice.R 
--base PGS000074.txt 
--target /home/sharedFolder/referenceData/ukb/imputed_genotypes/ukb_imp_chr#_v3,/home/sharedFolder/referenceData/ukb/imputed_genotypes/ukb_imp_chr1_v3.sample 
--type bgen
--snp SNP --chr CHR --bp BP --A1 A1 --A2 A2 --stat BETA --pvalue P
# --base-maf allelefrequency_effect:0.2
# --maf 0.01
--binary-target T 
--no-clump 
--fastscore
--ignore-fid 
--pheno /home/vsrinivasan75/cases_controls_new/pheno_white.txt
--cov /home/vsrinivasan75/cases_controls_new/covariates_white.txt
--cov-factor SEX 
--quantile 100 --quant-break 10,20,30,40,50,60,70,80,90,100 --quant-ref 50
--out /ukb_prs/colorectal_cancer/using_prsice/PGS000074/PGS000074_results 
--prsice PRSice/PRSice_linux

Rscript PRSice/PRSice.R 
--base PGS000785.txt 
--target /home/sharedFolder/referenceData/ukb/imputed_genotypes/ukb_imp_chr#_v3,/home/sharedFolder/referenceData/ukb/imputed_genotypes/ukb_imp_chr1_v3.sample 
--type bgen 
--snp SNP --chr CHR --bp BP --A1 A1 --A2 A2 --stat BETA --pvalue P
# --base-maf allelefrequency_effect:0.2
# --maf 0.01
--binary-target T 
--no-clump 
--fastscore
--ignore-fid 
--pheno /home/vsrinivasan75/cases_controls_new/pheno_white.txt
--cov /home/vsrinivasan75/cases_controls_new/covariates_white.txt
--cov-factor SEX 
--quantile 100 --quant-break 10,20,30,40,50,60,70,80,90,100  --quant-ref 50
--out /ukb_prs/colorectal_cancer/using_prsice/PGS000785/PGS000785_results 
--prsice PRSice/PRSice_linux