PRSice MAF and Filtering Step Slow

[zhanglucas]

Hi,

I'm trying to run PRSice on UKBB BGEN data, and I've noticed that the "Calculate MAF and perform filtering on target SNPs" step is extremely slow, to the point where I've let it run for nearly a week without this step finishing. I've also noticed that even with the --threads option set it's only using one thread in this step. Is there anything I can do to speed up this step?

Here are my run options:
PRSice2
--a1 A1
--a2 A2
--allow-inter
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--base /home/ukbiobank/PRS_SumStats_Pheno/rename_HF_bothsex_df_cleaned_reformat_without_NaN.assoc
--beta
--binary-target T
--bp BP
--chr CHR
--clump-kb 250kb
--clump-p 1.000000
--clump-r2 0.100000
--dose-thres 0.000000
--extract /home/[email protected]/ukbiobank/PRS_SumStats_Pheno/HF_snp_extract.txt
--hard
--hard-thres 0.100000
--id-delim "_"
--interval 5e-05
--lower 5e-08
--num-auto 22
--out HF_All_GBMI_with_HCM
--pheno /home/ukbiobank/PRS_SumStats_Pheno/HF_reordered_pheno.pheno
--print-snp
--pvalue P
--seed 2781250093
--snp SNP
--stat BETA
--target /home/ukbiobank/Genotypes/ukb21007_c#_b0_v1.recoded,/home/ukbiobank/Genotypes/ukb21007_c1_b0_v1.recoded.sample
--thread 23
--type bgen
--ultra
--upper 0.5

[choishingwan]

Unfortunately my implementation of the bgen format isn’t all that efficient. The best way would be first converting the bgen format to plink Usually the performance difference is not that high Sam

…

On Tue, Jul 9, 2024 at 1:02 PM Lucas Zhang ***@***.***> wrote: Hi, I'm trying to run PRSice on UKBB BGEN data, and I've noticed that the "Calculate MAF and perform filtering on target SNPs" step is extremely slow, to the point where I've let it run for nearly a week without this step finishing. I've also noticed that even with the --threads option set it's only using one thread in this step. Is there anything I can do to speed up this step? Here are my run options: PRSice2 --a1 A1 --a2 A2 --allow-inter --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 --base /home/ukbiobank/PRS_SumStats_Pheno/rename_HF_bothsex_df_cleaned_reformat_without_NaN.assoc --beta --binary-target T --bp BP --chr CHR --clump-kb 250kb --clump-p 1.000000 --clump-r2 0.100000 --dose-thres 0.000000 --extract ***@***.***/ukbiobank/PRS_SumStats_Pheno/HF_snp_extract.txt --hard --hard-thres 0.100000 --id-delim "_" --interval 5e-05 --lower 5e-08 --num-auto 22 --out HF_All_GBMI_with_HCM --pheno /home/ukbiobank/PRS_SumStats_Pheno/HF_reordered_pheno.pheno --print-snp --pvalue P --seed 2781250093 --snp SNP --stat BETA --target /home/ukbiobank/Genotypes/ukb21007_c#_b0_v1.recoded,/home/ukbiobank/Genotypes/ukb21007_c1_b0_v1.recoded.sample --thread 23 --type bgen --ultra --upper 0.5 — Reply to this email directly, view it on GitHub <#360>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYRU62CWZBVDKPZ45CLZLQJSDAVCNFSM6AAAAABKTIPLRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TQNZSG44TOMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>