Hi! I have a PGS file with the weights for each of the variants for a specific disease, CAD. The goal is to now calculate PRS scores for individuals in the UK Biobank genetic data. I have the plink bed, bim and fam files from the UK biobank data. What would be the steps to prepare the "Target data" from the uk biobank data?

I understand that using the PGS file as the "base data" requires adding a "fake" p-value column. I have tried using the bed, bim and fam files from uk biobank along with a GWAS file as the base data to which it gives: "Error: All sample has invalid phenotypes!",  "Errorr: No sample left" . What am I missing here? 


    > PRSice 2.3.5 (2021-04-06) 
    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)
    2021-06-02 18:41:16
    ./bin/PRSice \
        --a1 a1 \
        --a2 a2 \
        --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
        --base CAD_UKBIOBANK.gz \
        --beta  \
        --binary-target F \
        --bp bp \
        --chr chr \
        --extract PRSice.valid \
        --interval 5e-05 \
        --lower 5e-08 \
        --no-clump  \
        --num-auto 22 \
        --out PRSice \
        --pvalue pval \
        --seed 1999345467 \
        --snp oldID \
        --stat beta \
        --target chr# \
        --thread 4 \
        --upper 0.5
    
    Initializing Genotype file: chr# (bed) 
    
    Start processing CAD_UKBIOBANK 
    ================================================== 
    
    SNP extraction/exclusion list contains 5 columns, will 
    assume first column contains the SNP ID 
    
    Base file: /shared/Jenish/CAD_UKBIOBANK.gz 
    GZ file detected. Header of file is: 
    uniqid chr bp a1 a2 beta se pval N af oldID info zval 
    
    Reading 100.00%
    7947837 variant(s) observed in base file, with: 
    1202749 variant(s) excluded based on user input 
    6745088 total variant(s) included from base file 
    
    Loading Genotype info from target 
    ================================================== 
    
    488377 people (223459 male(s), 264780 female(s)) observed 
    488377 founder(s) included 
    
    181798 variant(s) not found in previous data 
    602458 variant(s) included 
    
    There are a total of 1 phenotype to process 
    
    Processing the 1 th phenotype 
    
    Error: All sample has invalid phenotypes! 
    Error: No sample left 
    
    Error: 
    Execution halted

    enter code here
You also need the `--no-clump --no-regress --bar-levels 1 --fastscore` parameters to tell PRSice not to perform clumping (as I supposed you are using pre-computed effect sizes, which has already accounted for LD) and not to perform the regression as you don't need to optimize the p-value thresholds

(I assume you are using PRSice as I recognize the error message)
