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) 
(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
    --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 
    --binary-target F 
    --bp bp 
    --chr chr 
    --extract PRSice.valid 
    --interval 5e-05 
    --lower 5e-08 
    --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 

Execution halted

enter code here

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