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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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Trying to run PRSice on files received by a collaborator but BGEN file is not being opened #348

Open varsh19 opened 1 year ago

varsh19 commented 1 year ago

I used the following command to calculate PRS of a sequenced file coming from a collaborator. I imputed the vcf file which gave me separate vcf files for each chromosome. I then converted them to bgen and generated bgi and sample files too.

Rscript ../PRSice/PRSice.R --base ../ukb_prs/PGS000785.txt --target ../tempus_files/202030905/207532750086_R08C02/#,../tempus_files/202030905/207532750086_R08C02/1.sample --type bgen --snp SNP --chr CHR --bp BP --A1 A1 --A2 A2 --stat BETA --pvalue P --binary-target T --no-clump --fastscore --ignore-fid --pheno ../tempus_files/202030905/207532750086_R08C02/207532750086_R08C02_pheno.txt --out 207532750086_R08C02_results --prsice ../PRSice/PRSice_linux

But I get the following error: Error: Cannot open bgen file ../tempus_files/202030905/207532750086_R08C02/1.bgen

The paths are all correct, but I cannot identify what the problem is. Please help me figure this out.

choishingwan commented 9 months ago

Did you check if you can see the file "../tempus_files/202030905/207532750086_R08C02/1.bgen" in the folder that your run the script?