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Published 20 hours ago • verified publisher icon choishingwan

#mismatching-snps

Open DM087 opened this issue 2 years ago • 9 comments

Hi Sam,

I am following your plink PRS tutorial and I have a couple of questions re mismatching-snps section https://choishingwan.github.io/PRS-Tutorial/target/#mismatching-snps .

  1. You say in the 'Note' section that 'Most PRS software will perform strand-flipping automatically, thus this step is usually not required.' I am trying to use plink --score and was wondering about running this step. Do you know if plink takes care of strand-flipping when using --score ?
  2. Should I be changing anything in the cases where SNP1 in the base data is A/C, and C/A in the target dataset? Do I need to change the .bim file in this case (or the effect allele in base data)?

Thank you for your help.

DM087 avatar Nov 19 '21 15:11 DM087