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Hi, I'm trying to generate PRS score based on pre-qc&clumped snplist in UKBiobank data using PRSice-2 and encounter the problem when reading bgen files.
My log here:
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)
2024-03-29 04:19:50
./PRSice
--a1 A1
--a2 A2
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--base result.txt
--base-info INFO:0.8
--beta
--binary-target F
--chr CHR
--clump-kb 250kb
--clump-p 1.000000
--clump-r2 0.100000
--interval 5e-05
--lower 5e-08
--num-auto 22
--out PRSice
--pvalue P
--seed 573448311
--snp SNP
--stat BETA
--thread 1
--upper 0.5
Error: You must provide a target file or a file containing
all target prefixs!
Error: You must provide a target file or a file containing all target prefixs!
However, I think I have provided the path of bgen files and my original codes reads:
Rscript ./PRSice.R
--dir .
--prsice ./PRSice
--base result.txt
--base-info INFO:0.8
--stat BETA
--type bgen
--target /mnt/project/Bulk/Imputation/'UKB imputation from genotype'/ukb22828_c#_b0_v3.bgen,/mnt/project/Bulk/Imputation/'UKB imputation from genotype'/ukb22828_c#_b0_v3.sample
--keep ./PRS_ID.txt
--remove ./rel.king.cutoff.in.id
--extract qc.clumps
--keep-ambig
--info 0.8
--pheno PRS_phe.txt
--cov PRS_cov.txt
--cov-factor sex,income
--thread max
--no-clump
--quantile 10
--out BD
I'm not sure what might be the problem causing this. I would be very appreciated if you can give me some advice.
Thank you!
The text was updated successfully, but these errors were encountered:
Hi, I'm trying to generate PRS score based on pre-qc&clumped snplist in UKBiobank data using PRSice-2 and encounter the problem when reading bgen files.
My log here:
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)
2024-03-29 04:19:50
./PRSice
--a1 A1
--a2 A2
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--base result.txt
--base-info INFO:0.8
--beta
--binary-target F
--chr CHR
--clump-kb 250kb
--clump-p 1.000000
--clump-r2 0.100000
--interval 5e-05
--lower 5e-08
--num-auto 22
--out PRSice
--pvalue P
--seed 573448311
--snp SNP
--stat BETA
--thread 1
--upper 0.5
Error: You must provide a target file or a file containing
all target prefixs!
Error: You must provide a target file or a file containing all target prefixs!
However, I think I have provided the path of bgen files and my original codes reads:
Rscript ./PRSice.R
--dir .
--prsice ./PRSice
--base result.txt
--base-info INFO:0.8
--stat BETA
--type bgen
--target /mnt/project/Bulk/Imputation/'UKB imputation from genotype'/ukb22828_c#_b0_v3.bgen,/mnt/project/Bulk/Imputation/'UKB imputation from genotype'/ukb22828_c#_b0_v3.sample
--keep ./PRS_ID.txt
--remove ./rel.king.cutoff.in.id
--extract qc.clumps
--keep-ambig
--info 0.8
--pheno PRS_phe.txt
--cov PRS_cov.txt
--cov-factor sex,income
--thread max
--no-clump
--quantile 10
--out BD
I'm not sure what might be the problem causing this. I would be very appreciated if you can give me some advice.
Thank you!
The text was updated successfully, but these errors were encountered: