search

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
185 stars 86 forks source link

All the variants are excluded, No valid variants #340

Closed msarguru closed 1 year ago

msarguru commented 1 year ago

Good day!

There are similar threads with the same issue. I have tried out all the different solutions, which did not help. Please see the log below,

Using PRSice version 2.3.5 And the SNPID from base file and from the target file matches, no duplicates, no special characters. Tried to follow https://www.biostars.org/p/9499252/ And I could see, 9612 variants have matching Rsids between the base and target file, allele, chr:pos details are also matching.

It would be great to have your suggestions.. Thanks

The log reads as.. PRSice/bin/PRSice \ --a1 Allele1 \ --a2 Allele2 \ --bar-levels 1e-05,0.001,0.01,0.1,0.5,1 \ --base basefile32K.forPRSICE \ --beta \ --binary-target F \ --bp POS \ --chr CHR \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.010000 \ --cov UKB.COVAR \ --fastscore \ --id-delim "tab" \ --num-auto 22 \ --out UKBK.forPRSICE.PRSice \ --perm 10000 \ --pheno ukbgen.PHE \ --pvalue pvalue \ --seed 3019675116 \ --snp MarkerName \ --stat Effect \ --target ukb668904.Set.chr# \ --thread 1

Initializing Genotype file: ukb668904.Set.chr# (bed)

Start processing UKBK

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

Base file: basefile32K.forPRSICE Header of file is: MarkerName CHR POS Allele1 Allele2 Effect StdErr pvalue

9714 variant(s) observed in base file, with: 9714 variant(s) excluded based on user input 0 total variant(s) included from base file

Error: No valid variant remaining

choishingwan commented 1 year ago

Are you sure that's the command? The log mentioned snp extraction/ exclusion file with 5 column, but I don't see a corresponding input in the command

On Mon, Sep 11, 2023, 1:22 PM msarguru @.***> wrote:

Assigned #340 https://github.com/choishingwan/PRSice/issues/340 to @choishingwan https://github.com/choishingwan.

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/340#event-10336994608, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYVZ7DN24OMS2MSQY6TXZ5CGDANCNFSM6AAAAAA4TVE66U . You are receiving this because you were assigned.Message ID: @.***>

msarguru commented 1 year ago

Thank you for the reply. I think there was feedback with the option --extract being used in the script. That removes all the valid SNPs.. omitting this option, the script runs fine..