Map PRS score to EID

Jinhan Zhu

Hi all,

After generating the PRS from the imputation data, how can we link the IID from plink output PRS file (which are -1, -2 ) to the EID in the phenotype data (EID/Patient ID) so we can run association test?  (Is gfetch to the local machine the only way to get the actual .sample file? )

Thanks for your help!!
 

Comments

2 comments

  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    I would expect to see the first few hundred rows of output with -1, -2 etc.  These correspond to participants who have withdrawn from the UKB.   I would expect the other rows to have EID in the IID column.   If this is not what you see, please explain a bit more about what plink command you ran.

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  • Comment author
    Jinhan Zhu

    Hi,

    Thanks for your advice, I checked the plink output and the original .sample file downloaded from the UKB, the IID are from -1 to -487409… The below is how I generated the PRS:

    1. convert the .bgen to plink2 trio files 

    plink2 --bgen UKB_imputation_all_chr.bgen ref-first --sample ukb22828_c1_b0_v3.sample --set-all-var-ids @:#\$r\$a --freq --make-pgen --out raw

    2. generate PRS
    plink2 --pfile raw --score PRScsx_SCZ_META_all_chr_withID.txt 7 4 6 cols=scoresums no-mean-imputation -out Fullset_PRS

    Thanks again for your help!

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