Error: No vairant remained!

[PyunJung-Min]

Hi,

I think i have a similar problem like Maleeha's below.. This is my log and there is 0 variants in the end..

Could you please help what is the problem? :)

Thanks always Jungmin

PRSice 2.3.2 (2020-07-10) 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) 2022-07-06 07:20:14 ./PRSice_linux \ --a1 A1 \ --a2 A2 \ --all-score \ --bar-levels 1e-05,0.0001,0.001,0.01,0.05,0.5,1 \ --base AD_sumstats_Jansenetal.txt \ --beta \ --binary-target F \ --bp BP \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --extract ROSMAP_PRS.valid \ --fastscore \ --ld 1000G_phase3_updated_eur \ --num-auto 22 \ --out ROSMAP_PRS \ --pvalue P \ --seed 2631138123 \ --snp SNP \ --stat BETA \ --target /BiO/Access/home/pyunmaster/TRS_brain/target \ --thread 1

Initializing Genotype file: /BiO/Access/home/pyunmaster/TRS_brain/target (bed)

Start processing AD_sumstats_Jansenetal ==================================================

SNP extraction/exclusion list contains 5 columns, will assume first column contains the SNP ID

Base file: AD_sumstats_Jansenetal.txt Header of file is: uniqID.a1a2 CHR BP A1 A2 SNP Z P Nsum Neff dir MAF BETA SE

13367299 variant(s) observed in base file, with: 1930219 variant(s) excluded based on user input 11437080 total variant(s) included from base file

Loading Genotype info from target ==================================================

233 people (0 male(s), 0 female(s)) observed 233 founder(s) included

64147439 variant(s) not found in previous data 0 variant(s) included

Error: No vairant remained!

[PyunJung-Min]

I found that my base and target data has different encoding for SNPs!