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



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