PRS

In this file, the rsID, chr_name, and chr_position fields are derived from GRCh37, while the hm_rsID, hm_chr, and hm_pos fields correspond to GRCh38.

PLINK v1.90b6.24 64-bit (6 Jun 2021)           www.cog-genomics.org/plink/1.9/
(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to demo_hg19_imput.log.
Options in effect:
  --allow-extra-chr
  --bfile demo_hg38_imput
  --chr 1-22
  --exclude LiftOver/hg38tohg19_rm.txt
  --make-bed
  --out demo_hg19_imput
  --update-chr LiftOver/hg38tohg19.txt 2 1
  --update-map LiftOver/hg38tohg19.txt 3 1
   
1031497 MB RAM detected; reserving 515748 MB for main workspace.
16537409 variants loaded from .bim file.
27719 people (0 males, 0 females, 27719 ambiguous) loaded from .fam.
Ambiguous sex IDs written to demo_hg19_imput.nosex .
--update-map: 16496680 values updated.
Warning: Base-pair positions are now unsorted!
--exclude: 16496680 variants remaining.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 27719 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.994176.
16496680 variants and 27719 people pass filters and QC.
Note: No phenotypes present.
--update-chr: 16496680 values updated.
--make-bed to demo_hg19_imput.bed + demo_hg19_imput.bim + demo_hg19_imput.fam
... done.

PLINK v1.90b6.24 64-bit (6 Jun 2021)           www.cog-genomics.org/plink/1.9/
(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to PRS/demo_hg19_imput_PGS002030.log.
Options in effect:
  --bfile demo_hg19_imput
  --out PRS/demo_hg19_imput_PGS002030
  --score materials/pgs/PGS002030_hmPOS_GRCh38.txt 1 4 6
 
1031497 MB RAM detected; reserving 515748 MB for main workspace.
16496116 variants loaded from .bim file.
2000 people (0 males, 0 females, 2000 ambiguous) loaded from .fam.
Ambiguous sex IDs written to PRS/demo_hg19_imput_PGS002030.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 2000 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.994153.
16496116 variants and 2000 people pass filters and QC.
Note: No phenotypes present.
Warning: 14515 lines skipped in --score file (14439 due to variant ID mismatch,
76 due to allele code mismatch); see PRS/demo_hg19_imput_PGS002030.nopred for
details.
--score: 148696 valid predictors loaded.
--score: Results written to PRS/demo_hg19_imput_PGS002030.profile .

PRSice 2.3.5 (2021-09-20)
https://github.com/choishingwan/PRSice
(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly
GNU General Public License v3
If you use PRSice in any published work, please cite:
Choi SW, O'Reilly PF.
PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.
GigaScience 8, no. 7 (July 1, 2019)
2025-04-14 15:21:34
tools/PRSice2/PRSice_linux \
    --a1 effect_allele \
    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
    --base materials/gwas/GCST90428597.h.tsv \
    --beta  \
    --binary-target T \
    --clump-kb 250kb \
    --clump-p 1.000000 \
    --clump-r2 0.100000 \
    --cov demo.phecov \
    --cov-col age,sex \
    --interval 5e-05 \
    --lower 5e-08 \
    --num-auto 22 \
    --out PRS/demo_hg19.prsice2 \
    --pheno demo.phecov \
    --pheno-col gout \
    --pvalue p_value \
    --seed 2013053753 \
    --snp rsid \
    --stat beta \
    --target demo_hg19 \
    --thread 1 \
    --upper 0.5
 
Initializing Genotype file: demo_hg19 (bed)
 
Start processing GCST90428597.h
==================================================
 
Base file: materials/gwas/GCST90428597.h.tsv
Header of file is:
 
chromosome      base_pair_location      effect_allele   other_allele    beta    standard_error  effect_allele_frequency p_value rsid    rs_id   n       hm_coordinate_c nversion       hm_code variant_id
 
Reading 100.00%
8714421 variant(s) observed in base file, with:
 
 Error: A total of 6 duplicated SNP ID detected out of
       8714415 input SNPs! Valid SNP ID (post --extract /
       --exclude, non-duplicated SNPs) stored at
       PRS/demo_hg19.prsice2.valid. You can avoid this
       error by using --extract PRS/demo_hg19.prsice2.valid 

PRSice 2.3.5 (2021-09-20)
https://github.com/choishingwan/PRSice
(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly
GNU General Public License v3
If you use PRSice in any published work, please cite:
Choi SW, O'Reilly PF.
PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.
GigaScience 8, no. 7 (July 1, 2019)
2025-04-14 15:40:31
./tools/PRSice2/PRSice_linux \
    --a1 effect_allele \
    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
    --base materials/gwas/GCST90428597.h.tsv \
    --beta  \
    --binary-target T \
    --clump-kb 250kb \
    --clump-p 1.000000 \
    --clump-r2 0.100000 \
    --cov demo.phecov \
    --cov-col age,sex \
    --extract PRS/demo_hg19.prsice2.valid \
    --interval 5e-05 \
    --lower 5e-08 \
    --num-auto 22 \
    --out PRS/demo_hg19.prsice2 \
    --pheno demo.phecov \
    --pheno-col gout \
    --pvalue p_value \
    --seed 685772835 \
    --snp rsid \
    --stat beta \
    --target demo_hg19 \
    --thread 1 \
    --upper 0.5
 
Initializing Genotype file: demo_hg19 (bed)
 
Start processing GCST90428597.h
==================================================
 
SNP extraction/exclusion list contains 4 columns, will
assume first column contains the SNP ID
 
Base file: materials/gwas/GCST90428597.h.tsv
Header of file is:
 
chromosome      base_pair_location      effect_allele   other_allele    beta    standard_error  effect_allele_frequency p_value rsid    rs_id   n       hm_coordinate_c nversion       hm_code variant_id
 
Reading 100.00%
8714421 variant(s) observed in base file, with:
12 variant(s) excluded based on user input
8714409 total variant(s) included from base file
 
Loading Genotype info from target
==================================================
 
2000 people (1384 male(s), 616 female(s)) observed
2000 founder(s) included
 
Warning: Currently not support haploid chromosome and sex
         chromosomes
 
28613 variant(s) not found in previous data
59 variant(s) with mismatch information
38747 ambiguous variant(s) excluded
564753 variant(s) included
 
Phenotype file: demo.phecov
Column Name of Sample ID: FID+IID
Note: If the phenotype file does not contain a header, the
column name will be displayed as the Sample ID which is
expected.
 
There are a total of 1 phenotype to process
 
Start performing clumping
 
Clumping Progress: 100.00%
Number of variant(s) after clumping : 96391
 
Processing the 1 th phenotype
 
gout is a binary phenotype
1000 control(s)
1000 case(s)
 
Processing the covariate file: demo.phecov
==============================
 
Include Covariates:
Name    Missing Number of levels
age     0       -
sex     0       -
 
After reading the covariate file, 2000 sample(s) included
in the analysis
 
Start Processing
Processing 100.00%

There are 1 region(s) with p-value less than 1e-5. Please
note that these results are inflated due to the overfitting
inherent in finding the best-fit PRS (but it's still best
to find the best-fit PRS!).
You can use the --perm option (see manual) to calculate an
empirical P-value.

 
Begin plotting
Current Rscript version = 2.3.3
Plotting Bar Plot
Plotting the high resolution plot

--ref_dir=materials/ld_ref/ldblk_1kg_eas
--bim_prefix=demo_hg19_imput
--sst_file=PRS/ckb.txt
--a=1
--b=0.5
--phi=None
--n_gwas=75956
--n_iter=1000
--n_burnin=500
--thin=5
--out_dir=PRS/prscs_
--chrom=['1']
--beta_std=FALSE
--write_psi=FALSE
--write_pst=FALSE
--seed=1
 
##### process chromosome 1 #####
... parse reference file: materials/ld_ref/ldblk_1kg_eas/snpinfo_1kg_hm3 ...
... 85604 SNPs on chromosome 1 read from materials/ld_ref/ldblk_1kg_eas/snpinfo_1kg_hm3 ...
... parse bim file: demo_hg19_imput.bim ...
... 1294576 SNPs on chromosome 1 read from demo_hg19_imput.bim ...
... parse sumstats file: PRS/ckb.txt ...
... 6850163 SNPs read from PRS/ckb.txt ...
... 78898 common SNPs in the reference, sumstats, and validation set ...
... parse reference LD on chromosome 1 ...
... MCMC ...
--- iter-100 ---
--- iter-200 ---
--- iter-300 ---
--- iter-400 ---
--- iter-500 ---
--- iter-600 ---
--- iter-700 ---
--- iter-800 ---
--- iter-900 ---
--- iter-1000 ---
... Estimated global shrinkage parameter: ...
... Done ...
 
...
 
##### process chromosome 22 #####
... parse reference file: materials/ld_ref/ldblk_1kg_eas/snpinfo_1kg_hm3 ...
... 14968 SNPs on chromosome 22 read from materials/ld_ref/ldblk_1kg_eas/snpinfo_1kg_hm3 ...
... parse bim file: demo_hg19_imput.bim ...
... 213675 SNPs on chromosome 22 read from demo_hg19_imput.bim ...
... parse sumstats file: PRS/ckb.txt ...
... 6850163 SNPs read from PRS/ckb.txt ...
... 12673 common SNPs in the reference, sumstats, and validation set ...
... parse reference LD on chromosome 22 ...
... MCMC ...
--- iter-100 ---
--- iter-200 ---
--- iter-300 ---
--- iter-400 ---
--- iter-500 ---
--- iter-600 ---
--- iter-700 ---
--- iter-800 ---
--- iter-900 ---
--- iter-1000 ---
... Estimated global shrinkage parameter: 9.25e-05 ...
... Done ...

PLINK v2.00a3.7LM 64-bit Intel (24 Oct 2022)   www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to PRS/demo_hg19_imput_prscs.log.
Options in effect:
  --bfile demo_hg19_imput
  --out PRS/demo_hg19_imput_prscs
  --score PRS/prscs_pst_eff_a1_b0.5_phiauto.txt 2 4 6 cols=+scoresums
 
Start time: Tue Apr 15 12:08:51 2025
1031497 MiB RAM detected; reserving 515748 MiB for main workspace.
Using up to 128 threads (change this with --threads).
2000 samples (0 females, 0 males, 2000 ambiguous; 2000 founders) loaded from
demo_hg19_imput.fam.
 
16496116 variants loaded from demo_hg19_imput.bim.
Note: No phenotype data present.
Calculating allele frequencies... done.
--score: 957101 variants processed.
--score: Results written to PRS/demo_hg19_imput_prscs.sscore .
End time: Tue Apr 15 12:08:55 2025

--ref_dir=materials/ld_ref
--bim_prefix=demo_hg19_imput
--sst_file=['PRS/ckb.txt', 'PRS/ukb.txt']
--a=1
--b=0.5
--phi=None
--n_gwas=[75956, 337159]
--pop=['EAS', 'EUR']
--n_iter=2000
--n_burnin=1000
--thin=5
--out_dir=PRS/prscsx
--out_name=demo
--chrom=['1', '2', '3', '4', '5']
--meta=TRUE
--write_pst=FALSE
--seed=1
 
*** 2 discovery populations detected ***
 
##### process chromosome 1 #####
... parse reference file: materials/ld_ref/snpinfo_mult_1kg_hm3 ...
... 109168 SNPs on chromosome 1 read from materials/ld_ref/snpinfo_mult_1kg_hm3 ...
... parse bim file: demo_hg19_imput.bim ...
... 1294576 SNPs on chromosome 1 read from demo_hg19_imput.bim ...
... parse EAS sumstats file: PRS/ckb.txt ...
... 6850163 SNPs read from PRS/ckb.txt ...
... 78898 common SNPs in the EAS reference, EAS sumstats, and validation set ...
... parse EUR sumstats file: PRS/ukb.txt ...
... 10894596 SNPs read from PRS/ukb.txt ...
... 82349 common SNPs in the EUR reference, EUR sumstats, and validation set ...
... parse EAS reference LD on chromosome 1 ...
... parse EUR reference LD on chromosome 1 ...
... align reference LD on chromosome 1 across populations ...
... 85336 valid SNPs across populations ...
... MCMC ...
--- iter-100 ---
--- iter-200 ---
--- iter-300 ---
--- iter-400 ---
--- iter-500 ---
--- iter-600 ---
--- iter-700 ---
--- iter-800 ---
--- iter-900 ---
--- iter-1000 ---
--- iter-1100 ---
--- iter-1200 ---
--- iter-1300 ---
--- iter-1400 ---
--- iter-1500 ---
--- iter-1600 ---
--- iter-1700 ---
--- iter-1800 ---
--- iter-1900 ---
--- iter-2000 ---
... Estimated global shrinkage parameter: 3.29e-05 ...
... Done ...
 
...
 
##### process chromosome 22 #####
... parse reference file: materials/ld_ref/snpinfo_mult_1kg_hm3 ...
... 18944 SNPs on chromosome 22 read from materials/ld_ref/snpinfo_mult_1kg_hm3 ...
... parse bim file: demo_hg19_imput.bim ...
... 213675 SNPs on chromosome 22 read from demo_hg19_imput.bim ...
... parse EAS sumstats file: PRS/ckb.txt ...
... 6850163 SNPs read from PRS/ckb.txt ...
... 12673 common SNPs in the EAS reference, EAS sumstats, and validation set ...
... parse EUR sumstats file: PRS/ukb.txt ...
... 10894596 SNPs read from PRS/ukb.txt ...
... 13399 common SNPs in the EUR reference, EUR sumstats, and validation set ...
... parse EAS reference LD on chromosome 22 ...
... parse EUR reference LD on chromosome 22 ...
... align reference LD on chromosome 22 across populations ...
... 13861 valid SNPs across populations ...
... MCMC ...
--- iter-100 ---
--- iter-200 ---
--- iter-300 ---
--- iter-400 ---
--- iter-500 ---
--- iter-600 ---
--- iter-700 ---
--- iter-800 ---
--- iter-900 ---
--- iter-1000 ---
--- iter-1100 ---
--- iter-1200 ---
--- iter-1300 ---
--- iter-1400 ---
--- iter-1500 ---
--- iter-1600 ---
--- iter-1700 ---
--- iter-1800 ---
--- iter-1900 ---
--- iter-2000 ---
... Estimated global shrinkage parameter: 2.48e-05 ...
... Done ...

demo_EAS_pst_eff_a1_b0.5_phiauto_chr10.txt
...
demo_EAS_pst_eff_a1_b0.5_phiauto_chr9.txt
demo_EUR_pst_eff_a1_b0.5_phiauto_chr10.txt
...
demo_EUR_pst_eff_a1_b0.5_phiauto_chr9.txt
demo_META_pst_eff_a1_b0.5_phiauto_chr10.txt
...
demo_META_pst_eff_a1_b0.5_phiauto_chr9.txt

PLINK v2.00a3.7LM 64-bit Intel (24 Oct 2022)   www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to PRS/demo_hg19_imput_prscsx_meta.log.
Options in effect:
  --bfile demo_hg19_imput
  --out PRS/demo_hg19_imput_prscsx_meta
  --score PRS/prscsx_pst_eff_a1_b0.5_phiauto_META.txt 2 4 6 cols=+scoresums
 
Start time: Wed Apr 16 14:22:52 2025
1031497 MiB RAM detected; reserving 515748 MiB for main workspace.
Using up to 128 threads (change this with --threads).
2000 samples (0 females, 0 males, 2000 ambiguous; 2000 founders) loaded from
demo_hg19_imput.fam.
 
16496116 variants loaded from demo_hg19_imput.bim.
Note: No phenotype data present.
Calculating allele frequencies... done.
--score: 1035617 variants processed.
--score: Results written to PRS/demo_hg19_imput_prscsx_meta.sscore .
End time: Wed Apr 16 14:22:56 2025